diff --git a/cmd/entire/cli/setup.go b/cmd/entire/cli/setup.go
index 13ae0f279..2ff5fbc6a 100644
--- a/cmd/entire/cli/setup.go
+++ b/cmd/entire/cli/setup.go
@@ -382,11 +382,20 @@ If Entire is already configured but disabled, this re-enables it.`,
 			// Check if we're in a git repository first - this is a prerequisite error,
 			// not a usage error, so we silence Cobra's output and use SilentError
 			// to prevent duplicate error output in main.go
-			if _, err := paths.WorktreeRoot(ctx); err != nil {
+			repoRoot, err := paths.WorktreeRoot(ctx)
+			if err != nil {
 				fmt.Fprintln(cmd.ErrOrStderr(), "Not a git repository. Please run 'entire enable' from within a git repository.")
 				return NewSilentError(errors.New("not a git repository"))
 			}
 
+			// Notify the user when running from a subdirectory.
+			// All path resolution uses paths.WorktreeRoot(ctx) which returns the
+			// correct repo root regardless of CWD, so no directory change is needed.
+			cwd, err := os.Getwd() //nolint:forbidigo // Need CWD to detect subdirectory
+			if err == nil && cwd != repoRoot {
+				fmt.Fprintf(cmd.ErrOrStderr(), "Note: Running from repository root (%s)\n\n", repoRoot)
+			}
+
 			if err := validateSetupFlags(opts.UseLocalSettings, opts.UseProjectSettings); err != nil {
 				return err
 			}