diff --git a/turbo/apps/web/src/db/migrations/0051_add_performance_indexes.sql b/turbo/apps/web/src/db/migrations/0051_add_performance_indexes.sql
new file mode 100644
index 000000000..dbe010a54
--- /dev/null
+++ b/turbo/apps/web/src/db/migrations/0051_add_performance_indexes.sql
@@ -0,0 +1,24 @@
+-- Migration: Add performance indexes for high-frequency queries
+-- Issue: #1284 - Add missing database indexes for high-frequency query columns
+
+-- agent_runs: Composite index for user listing with time-based sorting
+-- Optimizes: GET /v1/runs, user run listing queries
+CREATE INDEX "idx_agent_runs_user_created" ON "agent_runs"("user_id", "created_at" DESC);
+
+-- agent_runs: Partial index for cron cleanup job
+-- Optimizes: /api/cron/cleanup-sandboxes (finds running sandboxes with stale heartbeats)
+-- Only indexes rows where status='running', keeping index small
+CREATE INDEX "idx_agent_runs_running_heartbeat" ON "agent_runs"("last_heartbeat_at")
+  WHERE "status" = 'running';
+
+-- agent_runs: Partial index for schedule run history
+-- Optimizes: schedule-service.ts getRecentRuns query
+-- Only indexes scheduled runs (schedule_id IS NOT NULL)
+CREATE INDEX "idx_agent_runs_schedule_created" ON "agent_runs"("schedule_id", "created_at" DESC)
+  WHERE "schedule_id" IS NOT NULL;
+
+-- agent_sessions: Composite index for findOrCreate pattern
+-- Optimizes: agent-session-service.ts findOrCreate() method
+-- Covers queries with (userId, agentComposeId, artifactName) combinations
+CREATE INDEX "idx_agent_sessions_user_compose_artifact"
+  ON "agent_sessions"("user_id", "agent_compose_id", "artifact_name");
diff --git a/turbo/apps/web/src/db/schema/agent-run.ts b/turbo/apps/web/src/db/schema/agent-run.ts
index c44637c74..662721643 100644
--- a/turbo/apps/web/src/db/schema/agent-run.ts
+++ b/turbo/apps/web/src/db/schema/agent-run.ts
@@ -5,6 +5,7 @@ import {
   text,
   jsonb,
   timestamp,
+  index,
 } from "drizzle-orm/pg-core";
 import { agentComposeVersions } from "./agent-compose";
 
@@ -13,26 +14,41 @@ import { agentComposeVersions } from "./agent-compose";
  * Created when developer executes agent via SDK
  * References immutable compose version for reproducibility
  */
-export const agentRuns = pgTable("agent_runs", {
-  id: uuid("id").defaultRandom().primaryKey(),
-  userId: text("user_id").notNull(), // Clerk user ID - owner of this run
-  agentComposeVersionId: varchar("agent_compose_version_id", { length: 64 })
-    .references(() => agentComposeVersions.id)
-    .notNull(),
-  resumedFromCheckpointId: uuid("resumed_from_checkpoint_id"),
-  // References agent_schedules.id if this run was triggered by a schedule
-  // No FK constraint to avoid circular dependency with agent_schedules
-  scheduleId: uuid("schedule_id"),
-  status: varchar("status", { length: 20 }).notNull(),
-  prompt: text("prompt").notNull(),
-  vars: jsonb("vars"),
-  // Secret names for validation (values never stored - must be provided at runtime)
-  secretNames: jsonb("secret_names").$type<string[]>(),
-  sandboxId: varchar("sandbox_id", { length: 255 }),
-  result: jsonb("result"),
-  error: text("error"),
-  createdAt: timestamp("created_at").defaultNow().notNull(),
-  startedAt: timestamp("started_at"),
-  completedAt: timestamp("completed_at"),
-  lastHeartbeatAt: timestamp("last_heartbeat_at"),
-});
+export const agentRuns = pgTable(
+  "agent_runs",
+  {
+    id: uuid("id").defaultRandom().primaryKey(),
+    userId: text("user_id").notNull(), // Clerk user ID - owner of this run
+    agentComposeVersionId: varchar("agent_compose_version_id", { length: 64 })
+      .references(() => agentComposeVersions.id)
+      .notNull(),
+    resumedFromCheckpointId: uuid("resumed_from_checkpoint_id"),
+    // References agent_schedules.id if this run was triggered by a schedule
+    // No FK constraint to avoid circular dependency with agent_schedules
+    scheduleId: uuid("schedule_id"),
+    status: varchar("status", { length: 20 }).notNull(),
+    prompt: text("prompt").notNull(),
+    vars: jsonb("vars"),
+    // Secret names for validation (values never stored - must be provided at runtime)
+    secretNames: jsonb("secret_names").$type<string[]>(),
+    sandboxId: varchar("sandbox_id", { length: 255 }),
+    result: jsonb("result"),
+    error: text("error"),
+    createdAt: timestamp("created_at").defaultNow().notNull(),
+    startedAt: timestamp("started_at"),
+    completedAt: timestamp("completed_at"),
+    lastHeartbeatAt: timestamp("last_heartbeat_at"),
+  },
+  (table) => [
+    // Composite index for user listing with time-based sorting
+    index("idx_agent_runs_user_created").on(table.userId, table.createdAt),
+    // Partial index for cron cleanup (only running status)
+    index("idx_agent_runs_running_heartbeat")
+      .on(table.lastHeartbeatAt)
+      .where("status = 'running'" as never),
+    // Partial index for schedule history (only scheduled runs)
+    index("idx_agent_runs_schedule_created")
+      .on(table.scheduleId, table.createdAt)
+      .where("schedule_id IS NOT NULL" as never),
+  ],
+);
diff --git a/turbo/apps/web/src/db/schema/agent-session.ts b/turbo/apps/web/src/db/schema/agent-session.ts
index 77da91f93..6c1df4f12 100644
--- a/turbo/apps/web/src/db/schema/agent-session.ts
+++ b/turbo/apps/web/src/db/schema/agent-session.ts
@@ -5,6 +5,7 @@ import {
   text,
   timestamp,
   jsonb,
+  index,
 } from "drizzle-orm/pg-core";
 import { agentComposes } from "./agent-compose";
 import { conversations } from "./conversation";
@@ -20,24 +21,35 @@ import { conversations } from "./conversation";
  * - vars: Template variables for compose expansion
  * - secretNames: Secret names for validation (values never stored)
  */
-export const agentSessions = pgTable("agent_sessions", {
-  id: uuid("id").defaultRandom().primaryKey(),
-  userId: text("user_id").notNull(),
-  agentComposeId: uuid("agent_compose_id")
-    .references(() => agentComposes.id, { onDelete: "cascade" })
-    .notNull(),
-  // Immutable compose version ID (SHA-256 hash) fixed at session creation
-  // If null (legacy sessions), resolveSession falls back to HEAD version
-  agentComposeVersionId: varchar("agent_compose_version_id", { length: 255 }),
-  conversationId: uuid("conversation_id").references(() => conversations.id, {
-    onDelete: "set null",
-  }),
-  artifactName: varchar("artifact_name", { length: 255 }),
-  vars: jsonb("vars").$type<Record<string, string>>(),
-  // Secret names for validation (values never stored - must be provided at runtime)
-  secretNames: jsonb("secret_names").$type<string[]>(),
-  // Volume versions snapshot at session creation for reproducibility
-  volumeVersions: jsonb("volume_versions").$type<Record<string, string>>(),
-  createdAt: timestamp("created_at").defaultNow().notNull(),
-  updatedAt: timestamp("updated_at").defaultNow().notNull(),
-});
+export const agentSessions = pgTable(
+  "agent_sessions",
+  {
+    id: uuid("id").defaultRandom().primaryKey(),
+    userId: text("user_id").notNull(),
+    agentComposeId: uuid("agent_compose_id")
+      .references(() => agentComposes.id, { onDelete: "cascade" })
+      .notNull(),
+    // Immutable compose version ID (SHA-256 hash) fixed at session creation
+    // If null (legacy sessions), resolveSession falls back to HEAD version
+    agentComposeVersionId: varchar("agent_compose_version_id", { length: 255 }),
+    conversationId: uuid("conversation_id").references(() => conversations.id, {
+      onDelete: "set null",
+    }),
+    artifactName: varchar("artifact_name", { length: 255 }),
+    vars: jsonb("vars").$type<Record<string, string>>(),
+    // Secret names for validation (values never stored - must be provided at runtime)
+    secretNames: jsonb("secret_names").$type<string[]>(),
+    // Volume versions snapshot at session creation for reproducibility
+    volumeVersions: jsonb("volume_versions").$type<Record<string, string>>(),
+    createdAt: timestamp("created_at").defaultNow().notNull(),
+    updatedAt: timestamp("updated_at").defaultNow().notNull(),
+  },
+  (table) => [
+    // Composite index for findOrCreate pattern
+    index("idx_agent_sessions_user_compose_artifact").on(
+      table.userId,
+      table.agentComposeId,
+      table.artifactName,
+    ),
+  ],
+);