diff --git a/src/db/bootstrap.test.ts b/src/db/bootstrap.test.ts
new file mode 100644
index 0000000..402e3b8
--- /dev/null
+++ b/src/db/bootstrap.test.ts
@@ -0,0 +1,99 @@
+import { Database } from 'bun:sqlite';
+import fs from 'fs';
+import path from 'path';
+
+import { afterEach, describe, expect, it } from 'vitest';
+
+import { applyBaseSchema } from './base-schema.js';
+import { initializeDatabaseSchema } from './bootstrap.js';
+import { applyLegacySchemaMigrations } from './schema.js';
+
+function getAppliedSchemaMigrations(
+  database: Database,
+): Array<{ version: number; name: string }> {
+  return database
+    .prepare(
+      `SELECT version, name
+         FROM schema_migrations
+        ORDER BY version ASC`,
+    )
+    .all() as Array<{ version: number; name: string }>;
+}
+
+describe('initializeDatabaseSchema', () => {
+  const tempDirs: string[] = [];
+
+  afterEach(() => {
+    for (const tempDir of tempDirs.splice(0)) {
+      fs.rmSync(tempDir, { recursive: true, force: true });
+    }
+  });
+
+  it('records the legacy schema bundle as version 1 on a fresh database', () => {
+    const database = new Database(':memory:');
+
+    try {
+      initializeDatabaseSchema(database);
+
+      expect(getAppliedSchemaMigrations(database)).toEqual([
+        {
+          version: 1,
+          name: 'legacy_schema_bundle',
+        },
+      ]);
+    } finally {
+      database.close();
+    }
+  });
+
+  it('does not duplicate schema migration rows on repeated initialization', () => {
+    const database = new Database(':memory:');
+
+    try {
+      initializeDatabaseSchema(database);
+      initializeDatabaseSchema(database);
+
+      expect(getAppliedSchemaMigrations(database)).toEqual([
+        {
+          version: 1,
+          name: 'legacy_schema_bundle',
+        },
+      ]);
+    } finally {
+      database.close();
+    }
+  });
+
+  it('backfills schema migration tracking for an existing pre-versioned database', () => {
+    const tempDir = fs.mkdtempSync(
+      path.join('/tmp', 'ejclaw-schema-migrations-'),
+    );
+    tempDirs.push(tempDir);
+    const dbPath = path.join(tempDir, 'messages.db');
+    const legacyDb = new Database(dbPath);
+
+    try {
+      applyBaseSchema(legacyDb);
+      applyLegacySchemaMigrations(legacyDb, {
+        assistantName: 'Andy',
+      });
+    } finally {
+      legacyDb.close();
+    }
+
+    const reopened = new Database(dbPath);
+
+    try {
+      initializeDatabaseSchema(reopened);
+
+      expect(getAppliedSchemaMigrations(reopened)).toEqual([
+        {
+          version: 1,
+          name: 'legacy_schema_bundle',
+        },
+      ]);
+    } finally {
+      reopened.close();
+    }
+  });
+});
diff --git a/src/db/bootstrap.ts b/src/db/bootstrap.ts
index d836f7e..84511e1 100644
--- a/src/db/bootstrap.ts
+++ b/src/db/bootstrap.ts
@@ -4,7 +4,22 @@ import path from 'path';
 
 import { ASSISTANT_NAME, STORE_DIR } from '../config.js';
 import { applyBaseSchema } from './base-schema.js';
-import { applySchemaMigrations } from './schema.js';
+import { applyVersionedSchemaMigrations } from './migrations/index.js';
+
+function isFreshDatabase(database: Database): boolean {
+  const row = database
+    .prepare(
+      `
+        SELECT COUNT(*) AS count
+          FROM sqlite_master
+         WHERE type = 'table'
+           AND name NOT LIKE 'sqlite_%'
+           AND name != 'schema_migrations'
+      `,
+    )
+    .get() as { count: number };
+  return row.count === 0;
+}
 
 function setForeignKeys(database: Database, enabled: boolean): void {
   database.exec(`PRAGMA foreign_keys = ${enabled ? 'ON' : 'OFF'}`);
@@ -31,8 +46,10 @@ function assertNoForeignKeyViolations(database: Database): void {
 
 export function initializeDatabaseSchema(database: Database): void {
   setForeignKeys(database, false);
-  applyBaseSchema(database);
-  applySchemaMigrations(database, {
+  if (isFreshDatabase(database)) {
+    applyBaseSchema(database);
+  }
+  applyVersionedSchemaMigrations(database, {
     assistantName: ASSISTANT_NAME,
   });
   setForeignKeys(database, true);
diff --git a/src/db/migrations/001_legacy-schema-bundle.ts b/src/db/migrations/001_legacy-schema-bundle.ts
new file mode 100644
index 0000000..bc51eeb
--- /dev/null
+++ b/src/db/migrations/001_legacy-schema-bundle.ts
@@ -0,0 +1,67 @@
+import { applyBaseSchema } from '../base-schema.js';
+import { applyLegacySchemaMigrations } from '../schema.js';
+import type { SchemaMigrationDefinition } from './types.js';
+
+const LEGACY_BASELINE_TABLES = [
+  'chats',
+  'messages',
+  'message_sequence',
+  'work_items',
+  'scheduled_tasks',
+  'task_run_logs',
+  'router_state',
+  'sessions',
+  'paired_projects',
+  'paired_tasks',
+  'paired_workspaces',
+  'paired_turn_outputs',
+  'paired_turn_reservations',
+  'paired_turns',
+  'paired_turn_attempts',
+  'paired_task_execution_leases',
+  'channel_owner',
+  'room_settings',
+  'room_role_overrides',
+  'service_handoffs',
+  'memories',
+] as const;
+
+function tableExists(
+  database: Parameters<SchemaMigrationDefinition['apply']>[0],
+  tableName: string,
+): boolean {
+  const row = database
+    .prepare(
+      `
+        SELECT 1
+          FROM sqlite_master
+         WHERE type = 'table'
+           AND name = ?
+      `,
+    )
+    .get(tableName);
+  return row !== null && row !== undefined;
+}
+
+function requiresLegacyBaseSchemaPreflight(
+  database: Parameters<SchemaMigrationDefinition['apply']>[0],
+): boolean {
+  return LEGACY_BASELINE_TABLES.some(
+    (tableName) => !tableExists(database, tableName),
+  );
+}
+
+export const LEGACY_SCHEMA_BUNDLE_MIGRATION = {
+  version: 1,
+  name: 'legacy_schema_bundle',
+  alwaysRun: true,
+  apply(database, args) {
+    // Some pre-versioned test and upgrade fixtures contain only a subset of the
+    // current base tables. Re-establish the baseline before applying the legacy
+    // monolithic upgrade bundle.
+    if (requiresLegacyBaseSchemaPreflight(database)) {
+      applyBaseSchema(database);
+    }
+    applyLegacySchemaMigrations(database, args);
+  },
+} satisfies SchemaMigrationDefinition;
diff --git a/src/db/migrations/index.ts b/src/db/migrations/index.ts
new file mode 100644
index 0000000..1dc69f9
--- /dev/null
+++ b/src/db/migrations/index.ts
@@ -0,0 +1,66 @@
+import type { Database } from 'bun:sqlite';
+
+import { LEGACY_SCHEMA_BUNDLE_MIGRATION } from './001_legacy-schema-bundle.js';
+import type {
+  SchemaMigrationArgs,
+  SchemaMigrationDefinition,
+} from './types.js';
+
+const SCHEMA_MIGRATIONS_TABLE = 'schema_migrations';
+
+const ORDERED_SCHEMA_MIGRATIONS: readonly SchemaMigrationDefinition[] = [
+  LEGACY_SCHEMA_BUNDLE_MIGRATION,
+];
+
+function ensureSchemaMigrationsTable(database: Database): void {
+  database.exec(`
+    CREATE TABLE IF NOT EXISTS ${SCHEMA_MIGRATIONS_TABLE} (
+      version INTEGER PRIMARY KEY,
+      name TEXT NOT NULL,
+      applied_at TEXT NOT NULL DEFAULT (datetime('now'))
+    )
+  `);
+}
+
+function getAppliedSchemaVersions(database: Database): Set<number> {
+  const rows = database
+    .prepare(
+      `SELECT version
+         FROM ${SCHEMA_MIGRATIONS_TABLE}
+        ORDER BY version ASC`,
+    )
+    .all() as Array<{ version: number }>;
+  return new Set(rows.map((row) => row.version));
+}
+
+function recordAppliedSchemaMigration(
+  database: Database,
+  migration: SchemaMigrationDefinition,
+): void {
+  database
+    .prepare(
+      `INSERT INTO ${SCHEMA_MIGRATIONS_TABLE} (version, name)
+       VALUES (?, ?)`,
+    )
+    .run(migration.version, migration.name);
+}
+
+export function applyVersionedSchemaMigrations(
+  database: Database,
+  args: SchemaMigrationArgs,
+): void {
+  ensureSchemaMigrationsTable(database);
+  const appliedVersions = getAppliedSchemaVersions(database);
+
+  for (const migration of ORDERED_SCHEMA_MIGRATIONS) {
+    const alreadyApplied = appliedVersions.has(migration.version);
+    if (alreadyApplied && !migration.alwaysRun) {
+      continue;
+    }
+
+    migration.apply(database, args);
+    if (!alreadyApplied) {
+      recordAppliedSchemaMigration(database, migration);
+    }
+  }
+}
diff --git a/src/db/migrations/types.ts b/src/db/migrations/types.ts
new file mode 100644
index 0000000..912ad32
--- /dev/null
+++ b/src/db/migrations/types.ts
@@ -0,0 +1,12 @@
+import type { Database } from 'bun:sqlite';
+
+export interface SchemaMigrationArgs {
+  assistantName: string;
+}
+
+export interface SchemaMigrationDefinition {
+  version: number;
+  name: string;
+  alwaysRun?: boolean;
+  apply: (database: Database, args: SchemaMigrationArgs) => void;
+}
diff --git a/src/db/schema.ts b/src/db/schema.ts
index 6034278..3100af6 100644
--- a/src/db/schema.ts
+++ b/src/db/schema.ts
@@ -22,6 +22,10 @@ import {
   migrateSessionsTableToCompositePk,
 } from './sessions.js';
 
+// Legacy monolithic migration bundle kept for compatibility with databases
+// that predate ordered schema migration tracking. New schema changes belong in
+// src/db/migrations/*.
+
 function getTableColumns(database: Database, tableName: string): string[] {
   return (
     database.prepare(`PRAGMA table_info(${tableName})`).all() as Array<{
@@ -2568,7 +2572,7 @@ function backfillCanonicalWorkItemServiceIds(database: Database): void {
   tx(rows);
 }
 
-export function applySchemaMigrations(
+export function applyLegacySchemaMigrations(
   database: Database,
   args: {
     assistantName: string;
@@ -3154,3 +3158,6 @@ export function applySchemaMigrations(
     /* columns already exist */
   }
 }
+
+/** @deprecated New schema changes should be added under src/db/migrations/*. */
+export const applySchemaMigrations = applyLegacySchemaMigrations;