diff --git a/Cargo.lock b/Cargo.lock
index d58fca343..0b692ebf3 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -84,7 +84,7 @@ version = "1.1.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "40c48f72fd53cd289104fc64099abca73db4166ad86ea0b4341abe65af83dadc"
 dependencies = [
- "windows-sys 0.60.2",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -95,7 +95,7 @@ checksum = "291e6a250ff86cd4a820112fb8898808a366d8f9f58ce16d1f538353ad55747d"
 dependencies = [
  "anstyle",
  "once_cell_polyfill",
- "windows-sys 0.60.2",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -671,7 +671,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "39cab71617ae0d63f51a36d69f866391735b51691dbda63cf6f96d042b63efeb"
 dependencies = [
  "libc",
- "windows-sys 0.52.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -1326,7 +1326,7 @@ checksum = "3640c1c38b8e4e43584d8df18be5fc6b0aa314ce6ebf51b53313d4306cca8e46"
 dependencies = [
  "hermit-abi",
  "libc",
- "windows-sys 0.52.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -1611,7 +1611,7 @@ version = "0.50.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7957b9740744892f114936ab4a57b3f487491bbeafaf8083688b16841a4240e5"
 dependencies = [
- "windows-sys 0.59.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -2209,7 +2209,7 @@ dependencies = [
  "errno",
  "libc",
  "linux-raw-sys",
- "windows-sys 0.52.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -2516,7 +2516,6 @@ dependencies = [
  "cfg-if",
  "libc",
  "psm",
- "windows-sys 0.52.0",
  "windows-sys 0.59.0",
 ]
 
@@ -2608,7 +2607,7 @@ dependencies = [
  "getrandom 0.3.4",
  "once_cell",
  "rustix",
- "windows-sys 0.52.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -3202,7 +3201,7 @@ version = "0.1.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c2a7b1c03c876122aa43f3020e6c3c3ee5c05081c9a00739faf7503aeba10d22"
 dependencies = [
- "windows-sys 0.52.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
diff --git a/docs/cli.md b/docs/cli.md
index 56c9f9621..18b38eec2 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -60,7 +60,7 @@ prek install [OPTIONS] [HOOK|PROJECT]...
 <dl class="cli-reference"><dt id="prek-install--allow-missing-config"><a href="#prek-install--allow-missing-config"><code>--allow-missing-config</code></a></dt><dd><p>Allow a missing <code>pre-commit</code> configuration file</p>
 </dd><dt id="prek-install--cd"><a href="#prek-install--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-install--color"><a href="#prek-install--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -127,7 +127,7 @@ prek install-hooks [OPTIONS] [HOOK|PROJECT]...
 
 <dl class="cli-reference"><dt id="prek-install-hooks--cd"><a href="#prek-install-hooks--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-install-hooks--color"><a href="#prek-install-hooks--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -191,7 +191,7 @@ prek run [OPTIONS] [HOOK|PROJECT]...
 <dl class="cli-reference"><dt id="prek-run--all-files"><a href="#prek-run--all-files"><code>--all-files</code></a>, <code>-a</code></dt><dd><p>Run on all files in the repo</p>
 </dd><dt id="prek-run--cd"><a href="#prek-run--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-run--color"><a href="#prek-run--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -277,7 +277,7 @@ prek list [OPTIONS] [HOOK|PROJECT]...
 
 <dl class="cli-reference"><dt id="prek-list--cd"><a href="#prek-list--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-list--color"><a href="#prek-list--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -364,7 +364,7 @@ prek uninstall [OPTIONS]
 
 <dl class="cli-reference"><dt id="prek-uninstall--cd"><a href="#prek-uninstall--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-uninstall--color"><a href="#prek-uninstall--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -400,7 +400,7 @@ prek validate-config [OPTIONS] [CONFIG]...
 
 <dl class="cli-reference"><dt id="prek-validate-config--cd"><a href="#prek-validate-config--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-validate-config--color"><a href="#prek-validate-config--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -436,7 +436,7 @@ prek validate-manifest [OPTIONS] [MANIFEST]...
 
 <dl class="cli-reference"><dt id="prek-validate-manifest--cd"><a href="#prek-validate-manifest--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-validate-manifest--color"><a href="#prek-validate-manifest--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -467,7 +467,7 @@ prek sample-config [OPTIONS]
 
 <dl class="cli-reference"><dt id="prek-sample-config--cd"><a href="#prek-sample-config--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-sample-config--color"><a href="#prek-sample-config--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -500,7 +500,7 @@ prek auto-update [OPTIONS]
 <dl class="cli-reference"><dt id="prek-auto-update--bleeding-edge"><a href="#prek-auto-update--bleeding-edge"><code>--bleeding-edge</code></a></dt><dd><p>Update to the bleeding edge of the default branch instead of the latest tagged version</p>
 </dd><dt id="prek-auto-update--cd"><a href="#prek-auto-update--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-auto-update--color"><a href="#prek-auto-update--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -553,7 +553,7 @@ prek cache dir [OPTIONS]
 
 <dl class="cli-reference"><dt id="prek-cache-dir--cd"><a href="#prek-cache-dir--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-cache-dir--color"><a href="#prek-cache-dir--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -584,7 +584,7 @@ prek cache gc [OPTIONS]
 
 <dl class="cli-reference"><dt id="prek-cache-gc--cd"><a href="#prek-cache-gc--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-cache-gc--color"><a href="#prek-cache-gc--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -615,7 +615,7 @@ prek cache clean [OPTIONS]
 
 <dl class="cli-reference"><dt id="prek-cache-clean--cd"><a href="#prek-cache-clean--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-cache-clean--color"><a href="#prek-cache-clean--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -646,7 +646,7 @@ prek cache size [OPTIONS]
 
 <dl class="cli-reference"><dt id="prek-cache-size--cd"><a href="#prek-cache-size--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-cache-size--color"><a href="#prek-cache-size--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -683,7 +683,7 @@ prek init-template-dir [OPTIONS] <DIRECTORY>
 
 <dl class="cli-reference"><dt id="prek-init-template-dir--cd"><a href="#prek-init-template-dir--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-init-template-dir--color"><a href="#prek-init-template-dir--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -748,7 +748,7 @@ prek try-repo [OPTIONS] <REPO> [HOOK|PROJECT]...
 <dl class="cli-reference"><dt id="prek-try-repo--all-files"><a href="#prek-try-repo--all-files"><code>--all-files</code></a>, <code>-a</code></dt><dd><p>Run on all files in the repo</p>
 </dd><dt id="prek-try-repo--cd"><a href="#prek-try-repo--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-try-repo--color"><a href="#prek-try-repo--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
@@ -837,7 +837,7 @@ prek self update [OPTIONS] [TARGET_VERSION]
 
 <dl class="cli-reference"><dt id="prek-self-update--cd"><a href="#prek-self-update--cd"><code>--cd</code></a>, <code>-C</code> <i>dir</i></dt><dd><p>Change to directory before running</p>
 </dd><dt id="prek-self-update--color"><a href="#prek-self-update--color"><code>--color</code></a> <i>color</i></dt><dd><p>Whether to use color in output</p>
-<p>May also be set with the <code>PREK_COLOR</code> environment variable.</p><p>[default: auto]</p><p>Possible values:</p>
+<p>Possible values:</p>
 <ul>
 <li><code>auto</code>:  Enables colored output only when the output is going to a terminal or TTY with support</li>
 <li><code>always</code>:  Enables colored output regardless of the detected environment</li>
diff --git a/src/cli/mod.rs b/src/cli/mod.rs
index 96a39112e..8b2c1695b 100644
--- a/src/cli/mod.rs
+++ b/src/cli/mod.rs
@@ -9,9 +9,9 @@ use clap_complete::engine::ArgValueCompleter;
 use serde::{Deserialize, Serialize};
 
 use prek_consts::CONFIG_FILE;
-use prek_consts::env_vars::EnvVars;
 
 use crate::config::{HookType, Language, Stage};
+use crate::settings::{CliOverrides, ColorChoice};
 
 mod auto_update;
 mod cache_clean;
@@ -72,28 +72,6 @@ impl From<ExitStatus> for ExitCode {
     }
 }
 
-#[derive(Debug, Copy, Clone, clap::ValueEnum)]
-pub enum ColorChoice {
-    /// Enables colored output only when the output is going to a terminal or TTY with support.
-    Auto,
-
-    /// Enables colored output regardless of the detected environment.
-    Always,
-
-    /// Disables colored output.
-    Never,
-}
-
-impl From<ColorChoice> for anstream::ColorChoice {
-    fn from(value: ColorChoice) -> Self {
-        match value {
-            ColorChoice::Auto => Self::Auto,
-            ColorChoice::Always => Self::Always,
-            ColorChoice::Never => Self::Never,
-        }
-    }
-}
-
 const STYLES: Styles = Styles::styled()
     .header(AnsiColor::Green.on_default().effects(Effects::BOLD))
     .usage(AnsiColor::Green.on_default().effects(Effects::BOLD))
@@ -144,14 +122,8 @@ pub(crate) struct GlobalArgs {
     pub(crate) cd: Option<PathBuf>,
 
     /// Whether to use color in output.
-    #[arg(
-        global = true,
-        long,
-        value_enum,
-        env = EnvVars::PREK_COLOR,
-        default_value_t = ColorChoice::Auto,
-    )]
-    pub(crate) color: ColorChoice,
+    #[arg(global = true, long, value_enum)]
+    pub(crate) color: Option<ColorChoice>,
 
     /// Refresh all cached data.
     #[arg(global = true, long)]
@@ -198,6 +170,13 @@ pub(crate) struct GlobalArgs {
     pub show_settings: bool,
 }
 
+impl GlobalArgs {
+    /// Build CLI overrides from the parsed arguments.
+    pub fn cli_overrides(&self) -> CliOverrides {
+        CliOverrides::new().color(self.color)
+    }
+}
+
 #[derive(Debug, Subcommand)]
 pub(crate) enum Command {
     /// Install the prek git hook.
diff --git a/src/main.rs b/src/main.rs
index 7f3be6990..6cda7ab34 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -23,6 +23,7 @@ use crate::cli::{CacheCommand, CacheNamespace, Cli, Command, ExitStatus};
 use crate::cli::{SelfCommand, SelfNamespace, SelfUpdateArgs};
 use crate::printer::Printer;
 use crate::run::USE_COLOR;
+use crate::settings::Settings;
 use crate::store::Store;
 
 mod archive;
@@ -40,6 +41,7 @@ mod process;
 #[cfg(all(unix, feature = "profiler"))]
 mod profiler;
 mod run;
+pub mod settings;
 mod store;
 mod version;
 mod warnings;
@@ -141,7 +143,20 @@ async fn run(mut cli: Cli) -> Result<ExitStatus> {
     // Enabled ANSI colors on Windows.
     let _ = anstyle_query::windows::enable_ansi_colors();
 
-    ColorChoice::write_global(cli.globals.color.into());
+    // Determine working directory early (--cd flag or current dir)
+    let working_dir = cli
+        .globals
+        .cd
+        .clone()
+        .unwrap_or_else(|| std::env::current_dir().unwrap_or_default());
+
+    // Initialize settings from all sources (env vars, pyproject.toml, CLI overrides)
+    Settings::init_with_cli(&working_dir, cli.globals.cli_overrides());
+
+    let settings = Settings::get();
+
+    // Set color from resolved settings (CLI > pyproject.toml > env var > default)
+    ColorChoice::write_global(settings.resolved_color().into());
 
     let store = Store::from_settings()?;
     let log_file = LogFile::from_args(cli.globals.log_file.clone(), cli.globals.no_log_file);
diff --git a/src/settings.rs b/src/settings.rs
new file mode 100644
index 000000000..3e02bd5b2
--- /dev/null
+++ b/src/settings.rs
@@ -0,0 +1,362 @@
+//! Unified configuration settings for prek.
+//!
+//! Settings are resolved from multiple sources with the following precedence (highest to lowest):
+//! 1. CLI flags (merged via `CliOverrides`)
+//! 2. `pyproject.toml` `[tool.prek]` section
+//! 3. Environment variables (`PREK_*`)
+//! 4. Built-in defaults
+
+use std::path::{Path, PathBuf};
+use std::sync::{LazyLock, RwLock};
+
+use prek_consts::env_vars::EnvVars;
+use serde::Deserialize;
+
+/// Global settings instance, initialized lazily.
+///
+/// Call `Settings::init_with_cli()` early in main to set the working directory,
+/// or it will default to the current directory.
+static SETTINGS: LazyLock<RwLock<Settings>> = LazyLock::new(|| RwLock::new(Settings::default()));
+
+/// Check if settings have been initialized
+static INITIALIZED: LazyLock<RwLock<bool>> = LazyLock::new(|| RwLock::new(false));
+
+/// Prek configuration settings.
+#[derive(Debug, Clone, Default, PartialEq, Eq)]
+#[allow(clippy::struct_excessive_bools)]
+pub struct Settings {
+    /// Hook IDs to skip (equivalent to `PREK_SKIP`).
+    pub skip: Vec<String>,
+    /// Override the prek data directory (equivalent to `PREK_HOME`).
+    pub home: Option<PathBuf>,
+    /// Control colored output: "auto", "always", or "never" (equivalent to `PREK_COLOR`).
+    pub color: Option<ColorChoice>,
+    /// Allow running without a `.pre-commit-config.yaml` (equivalent to `PREK_ALLOW_NO_CONFIG`).
+    pub allow_no_config: bool,
+    /// Disable parallelism for installs and runs (equivalent to `PREK_NO_CONCURRENCY`).
+    pub no_concurrency: bool,
+    /// Disable Rust-native built-in hooks (equivalent to `PREK_NO_FAST_PATH`).
+    pub no_fast_path: bool,
+    /// Control how uv is installed (equivalent to `PREK_UV_SOURCE`).
+    pub uv_source: Option<String>,
+    /// Use system's trusted store instead of bundled roots (equivalent to `PREK_NATIVE_TLS`).
+    pub native_tls: bool,
+    /// Container runtime to use: "auto", "docker", or "podman" (equivalent to `PREK_CONTAINER_RUNTIME`).
+    pub container_runtime: Option<ContainerRuntime>,
+}
+
+/// Settings as parsed from pyproject.toml `[tool.prek]`
+#[derive(Debug, Default, Deserialize)]
+#[serde(default, rename_all = "kebab-case")]
+#[allow(clippy::struct_excessive_bools)]
+struct PyProjectSettings {
+    skip: Vec<String>,
+    home: Option<PathBuf>,
+    color: Option<ColorChoice>,
+    allow_no_config: bool,
+    no_concurrency: bool,
+    no_fast_path: bool,
+    uv_source: Option<String>,
+    native_tls: bool,
+    container_runtime: Option<ContainerRuntime>,
+}
+
+/// Wrapper to extract `[tool.prek]` from pyproject.toml
+#[derive(Debug, Deserialize)]
+struct PyProjectToml {
+    tool: Option<PyProjectTool>,
+}
+
+#[derive(Debug, Deserialize)]
+struct PyProjectTool {
+    prek: Option<PyProjectSettings>,
+}
+
+/// Color output choice.
+#[derive(Debug, Clone, Copy, Default, PartialEq, Eq, Deserialize, clap::ValueEnum)]
+#[serde(rename_all = "lowercase")]
+pub enum ColorChoice {
+    /// Enables colored output only when the output is going to a terminal or TTY with support.
+    #[default]
+    Auto,
+    /// Enables colored output regardless of the detected environment.
+    Always,
+    /// Disables colored output.
+    Never,
+}
+
+impl std::fmt::Display for ColorChoice {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::Auto => write!(f, "auto"),
+            Self::Always => write!(f, "always"),
+            Self::Never => write!(f, "never"),
+        }
+    }
+}
+
+impl From<ColorChoice> for anstream::ColorChoice {
+    fn from(value: ColorChoice) -> Self {
+        match value {
+            ColorChoice::Auto => Self::Auto,
+            ColorChoice::Always => Self::Always,
+            ColorChoice::Never => Self::Never,
+        }
+    }
+}
+
+impl std::str::FromStr for ColorChoice {
+    type Err = String;
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        match s.to_lowercase().as_str() {
+            "auto" => Ok(Self::Auto),
+            "always" => Ok(Self::Always),
+            "never" => Ok(Self::Never),
+            _ => Err(format!("invalid color choice: {s}")),
+        }
+    }
+}
+
+/// Container runtime choice.
+#[derive(Debug, Clone, Copy, Default, PartialEq, Eq, Deserialize, clap::ValueEnum)]
+#[serde(rename_all = "lowercase")]
+pub enum ContainerRuntime {
+    /// Auto-detect available runtime.
+    #[default]
+    Auto,
+    /// Use Docker.
+    Docker,
+    /// Use Podman.
+    Podman,
+}
+
+impl std::str::FromStr for ContainerRuntime {
+    type Err = String;
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        match s.to_lowercase().as_str() {
+            "auto" => Ok(Self::Auto),
+            "docker" => Ok(Self::Docker),
+            "podman" => Ok(Self::Podman),
+            _ => Err(format!("invalid container runtime: {s}")),
+        }
+    }
+}
+
+impl std::fmt::Display for ContainerRuntime {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            Self::Auto => write!(f, "auto"),
+            Self::Docker => write!(f, "docker"),
+            Self::Podman => write!(f, "podman"),
+        }
+    }
+}
+
+/// CLI overrides that take highest precedence.
+///
+/// This struct contains only the fields that can be set via CLI flags.
+/// Fields are all optional - `None` means "use value from other sources".
+#[derive(Copy, Debug, Clone, Default)]
+pub struct CliOverrides {
+    pub color: Option<ColorChoice>,
+}
+
+impl CliOverrides {
+    pub fn new() -> Self {
+        Self::default()
+    }
+
+    #[must_use]
+    pub fn color(mut self, color: Option<ColorChoice>) -> Self {
+        self.color = color;
+        self
+    }
+}
+
+impl Settings {
+    /// Initialize settings with CLI overrides.
+    ///
+    /// This should be called early in `main()` before any settings are accessed.
+    pub fn init_with_cli(working_dir: &Path, cli: CliOverrides) {
+        let settings = Self::load(working_dir, cli);
+        *SETTINGS.write().expect("settings lock poisoned") = settings;
+        *INITIALIZED.write().expect("initialized lock poisoned") = true;
+    }
+
+    /// Get the global settings instance.
+    ///
+    /// If settings haven't been initialized, this will initialize them
+    /// using the current directory.
+    pub fn get() -> Settings {
+        {
+            let initialized = *INITIALIZED.read().expect("initialized lock poisoned");
+            if !initialized {
+                let cwd = std::env::current_dir().unwrap_or_default();
+                Self::init_with_cli(&cwd, CliOverrides::default());
+            }
+        }
+        SETTINGS.read().expect("settings lock poisoned").clone()
+    }
+
+    /// Load and merge settings from all sources.
+    fn load(start_dir: &Path, cli: CliOverrides) -> Self {
+        // Start with pyproject.toml settings (or defaults)
+        let pyproject = Self::load_pyproject(start_dir).unwrap_or_default();
+
+        // Layer env vars on top, then CLI
+        Settings {
+            skip: env_list("PREK_SKIP")
+                .or_else(|| env_list("SKIP"))
+                .unwrap_or(pyproject.skip),
+            home: env_path("PREK_HOME").or(pyproject.home),
+            color: cli
+                .color
+                .or_else(|| env_parse::<ColorChoice>("PREK_COLOR"))
+                .or(pyproject.color),
+            allow_no_config: env_bool("PREK_ALLOW_NO_CONFIG").unwrap_or(pyproject.allow_no_config),
+            no_concurrency: env_bool("PREK_NO_CONCURRENCY").unwrap_or(pyproject.no_concurrency),
+            no_fast_path: env_bool("PREK_NO_FAST_PATH").unwrap_or(pyproject.no_fast_path),
+            uv_source: env_string("PREK_UV_SOURCE").or(pyproject.uv_source),
+            native_tls: env_bool("PREK_NATIVE_TLS").unwrap_or(pyproject.native_tls),
+            container_runtime: env_parse("PREK_CONTAINER_RUNTIME").or(pyproject.container_runtime),
+        }
+    }
+
+    /// Walk up the directory tree to find and parse pyproject.toml
+    fn load_pyproject(start_dir: &Path) -> Option<PyProjectSettings> {
+        let mut dir = Some(start_dir);
+        while let Some(d) = dir {
+            if let Ok(content) = std::fs::read_to_string(d.join("pyproject.toml")) {
+                if let Ok(parsed) = toml::from_str::<PyProjectToml>(&content) {
+                    if let Some(settings) = parsed.tool.and_then(|t| t.prek) {
+                        return Some(settings);
+                    }
+                }
+            }
+            dir = d.parent();
+        }
+        None
+    }
+
+    /// Check if a hook should be skipped.
+    pub fn should_skip(&self, hook_id: &str) -> bool {
+        self.skip.iter().any(|s| s == hook_id)
+    }
+
+    /// Get the resolved color choice.
+    pub fn resolved_color(&self) -> ColorChoice {
+        self.color.unwrap_or_default()
+    }
+
+    /// Get the resolved container runtime.
+    pub fn resolved_container_runtime(&self) -> ContainerRuntime {
+        self.container_runtime.unwrap_or_default()
+    }
+}
+
+// Simple env var helpers
+fn env_string(key: &str) -> Option<String> {
+    EnvVars::var(key).ok()
+}
+
+fn env_path(key: &str) -> Option<PathBuf> {
+    env_string(key).map(PathBuf::from)
+}
+
+fn env_bool(key: &str) -> Option<bool> {
+    EnvVars::var_as_bool(key)
+}
+
+fn env_parse<T: std::str::FromStr>(key: &str) -> Option<T> {
+    env_string(key).and_then(|s| s.parse().ok())
+}
+
+fn env_list(key: &str) -> Option<Vec<String>> {
+    env_string(key).map(|s| {
+        s.split(',')
+            .map(|p| p.trim().to_string())
+            .filter(|p| !p.is_empty())
+            .collect()
+    })
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use std::io::Write;
+    use tempfile::TempDir;
+
+    #[test]
+    fn test_default_settings() {
+        let settings = Settings::default();
+        assert!(settings.skip.is_empty());
+        assert!(settings.home.is_none());
+        assert!(!settings.no_concurrency);
+    }
+
+    #[test]
+    fn test_pyproject_loading() {
+        let dir = TempDir::new().unwrap();
+        let pyproject = dir.path().join("pyproject.toml");
+
+        let mut file = std::fs::File::create(&pyproject).unwrap();
+        write!(
+            file,
+            r#"
+[tool.prek]
+skip = ["black", "ruff"]
+no-concurrency = true
+color = "always"
+"#
+        )
+        .unwrap();
+
+        let settings = Settings::load(dir.path(), CliOverrides::default());
+        assert_eq!(settings.skip, vec!["black", "ruff"]);
+        assert!(settings.no_concurrency);
+        assert_eq!(settings.color, Some(ColorChoice::Always));
+    }
+
+    #[test]
+    fn test_walks_up_directory_tree() {
+        let dir = TempDir::new().unwrap();
+        let pyproject = dir.path().join("pyproject.toml");
+
+        let mut file = std::fs::File::create(&pyproject).unwrap();
+        write!(
+            file,
+            r#"
+[tool.prek]
+skip = ["parent-hook"]
+"#
+        )
+        .unwrap();
+
+        std::fs::create_dir_all(dir.path().join("subdir/nested")).unwrap();
+
+        let settings = Settings::load(&dir.path().join("subdir/nested"), CliOverrides::default());
+        assert_eq!(settings.skip, vec!["parent-hook"]);
+    }
+
+    #[test]
+    fn test_cli_overrides_pyproject() {
+        let dir = TempDir::new().unwrap();
+        let pyproject = dir.path().join("pyproject.toml");
+
+        let mut file = std::fs::File::create(&pyproject).unwrap();
+        write!(
+            file,
+            r#"
+[tool.prek]
+color = "auto"
+"#
+        )
+        .unwrap();
+
+        let settings = Settings::load(
+            dir.path(),
+            CliOverrides::new().color(Some(ColorChoice::Always)),
+        );
+        assert_eq!(settings.color, Some(ColorChoice::Always));
+    }
+}
diff --git a/src/store.rs b/src/store.rs
index 9ba56352a..39b3a2761 100644
--- a/src/store.rs
+++ b/src/store.rs
@@ -9,13 +9,12 @@ use futures::StreamExt;
 use thiserror::Error;
 use tracing::{debug, warn};
 
-use prek_consts::env_vars::EnvVars;
-
 use crate::config::RemoteRepo;
 use crate::fs::LockedFile;
 use crate::git::clone_repo;
 use crate::hook::InstallInfo;
 use crate::run::CONCURRENCY;
+use crate::settings::Settings;
 use crate::workspace::HookInitReporter;
 
 #[derive(Debug, Error)]
@@ -41,13 +40,15 @@ impl Store {
         Self { path: path.into() }
     }
 
-    /// Create a store from environment variables or default paths.
+    /// Create a store from settings or default paths.
     pub(crate) fn from_settings() -> Result<Self, Error> {
-        let path = if let Some(path) = EnvVars::var_os(EnvVars::PREK_HOME) {
-            Some(path.into())
+        let settings = Settings::get();
+
+        let path = if let Some(home) = settings.home {
+            Some(home)
         } else {
             etcetera::choose_base_strategy()
-                .map(|path| path.cache_dir().join("prek"))
+                .map(|strategy| strategy.cache_dir().join("prek"))
                 .ok()
         };