diff --git a/README.md b/README.md
index 016444ee..4500a337 100644
--- a/README.md
+++ b/README.md
@@ -979,6 +979,7 @@ OmniRoute is available as a public Docker image on [Docker Hub](https://hub.dock
 docker run -d \
   --name omniroute \
   --restart unless-stopped \
+  --stop-timeout 40 \
   -p 20128:20128 \
   -v omniroute-data:/app/data \
   diegosouzapw/omniroute:latest
@@ -993,6 +994,7 @@ cp .env.example .env
 docker run -d \
   --name omniroute \
   --restart unless-stopped \
+  --stop-timeout 40 \
   --env-file .env \
   -p 20128:20128 \
   -v omniroute-data:/app/data \
@@ -1016,6 +1018,8 @@ Notes:
 - Quick Tunnel URLs are temporary and change after every restart.
 - Managed install currently supports Linux, macOS, and Windows on `x64` / `arm64`.
 - Docker images bundle system CA roots and pass them to managed `cloudflared`, which avoids TLS trust failures when the tunnel bootstraps inside the container.
+- SQLite runs in WAL mode. `docker stop` should be allowed to finish so OmniRoute can checkpoint the latest changes back into `storage.sqlite`.
+- The bundled Compose files already set a 40s stop grace period. If you run the image directly, keep `--stop-timeout 40` (or similar) so manual stops do not cut off shutdown cleanup.
 - Set `CLOUDFLARED_BIN=/absolute/path/to/cloudflared` if you want OmniRoute to use an existing binary instead of downloading one.
 
 **Using Docker Compose with Caddy (HTTPS Auto-TLS):**
diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml
index 5674b10c..cb86dc57 100644
--- a/docker-compose.prod.yml
+++ b/docker-compose.prod.yml
@@ -19,6 +19,7 @@ services:
       target: runner-cli
     image: omniroute:prod
     restart: unless-stopped
+    stop_grace_period: 40s
     env_file: .env
     environment:
       - NODE_ENV=production
diff --git a/docker-compose.yml b/docker-compose.yml
index 8bc975b3..96e5be2c 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -17,6 +17,7 @@
 
 x-common: &common
   restart: unless-stopped
+  stop_grace_period: 40s
   env_file: .env
   environment:
     - DATA_DIR=/app/data # Must match the volume mount below
diff --git a/docs/i18n/zh-CN/README.md b/docs/i18n/zh-CN/README.md
index a28f829e..56779901 100644
--- a/docs/i18n/zh-CN/README.md
+++ b/docs/i18n/zh-CN/README.md
@@ -983,6 +983,7 @@ OmniRoute is available as a public Docker image on [Docker Hub](https://hub.dock
 docker run -d \
   --name omniroute \
   --restart unless-stopped \
+  --stop-timeout 40 \
   -p 20128:20128 \
   -v omniroute-data:/app/data \
   diegosouzapw/omniroute:latest
@@ -997,6 +998,7 @@ cp .env.example .env
 docker run -d \
   --name omniroute \
   --restart unless-stopped \
+  --stop-timeout 40 \
   --env-file .env \
   -p 20128:20128 \
   -v omniroute-data:/app/data \
@@ -1020,6 +1022,8 @@ Notes:
 - Quick Tunnel URLs are temporary and change after every restart.
 - Managed install currently supports Linux, macOS, and Windows on `x64` / `arm64`.
 - Docker images bundle system CA roots and pass them to managed `cloudflared`, which avoids TLS trust failures when the tunnel bootstraps inside the container.
+- SQLite uses WAL mode. Let `docker stop` finish cleanly so OmniRoute can checkpoint the latest changes back into `storage.sqlite`.
+- The bundled Compose files already use a 40s stop grace period. If you run the image directly, keep `--stop-timeout 40` (or similar) so manual stops do not interrupt shutdown cleanup.
 - Set `CLOUDFLARED_BIN=/absolute/path/to/cloudflared` if you want OmniRoute to use an existing binary instead of downloading one.
 
 **Using Docker Compose with Caddy (HTTPS Auto-TLS):**
diff --git a/src/app/api/restart/route.ts b/src/app/api/restart/route.ts
index 909ccf44..74f1d3f9 100644
--- a/src/app/api/restart/route.ts
+++ b/src/app/api/restart/route.ts
@@ -1,9 +1,9 @@
 import { NextResponse } from "next/server";
 
 export async function POST() {
-  // Graceful restart: exit with code 0 so the process manager (pm2/systemd) restarts
+  // Graceful restart: SIGTERM flows through the shutdown handler before the process manager restarts
   setTimeout(() => {
-    process.exit(0);
+    process.kill(process.pid, "SIGTERM");
   }, 500);
 
   return NextResponse.json({ status: "restarting" });
diff --git a/src/app/api/shutdown/route.ts b/src/app/api/shutdown/route.ts
index ce713401..eddf43c4 100644
--- a/src/app/api/shutdown/route.ts
+++ b/src/app/api/shutdown/route.ts
@@ -4,7 +4,7 @@ export async function POST() {
   const response = NextResponse.json({ success: true, message: "Shutting down..." });
 
   setTimeout(() => {
-    process.exit(0);
+    process.kill(process.pid, "SIGTERM");
   }, 500);
 
   return response;
diff --git a/src/lib/db/core.ts b/src/lib/db/core.ts
index 14d9ee84..90e66d44 100644
--- a/src/lib/db/core.ts
+++ b/src/lib/db/core.ts
@@ -12,6 +12,7 @@ import { runMigrations } from "./migrationRunner";
 
 type SqliteDatabase = import("better-sqlite3").Database;
 type JsonRecord = Record<string, unknown>;
+type CheckpointMode = "PASSIVE" | "FULL" | "RESTART" | "TRUNCATE";
 
 // ──────────────── Environment Detection ────────────────
 
@@ -323,6 +324,12 @@ function setDb(db: SqliteDatabase | null): void {
   }
 }
 
+function checkpointDb(db: SqliteDatabase, mode: CheckpointMode = "TRUNCATE"): boolean {
+  if (isCloud || isBuildPhase || !SQLITE_FILE) return false;
+  db.pragma(`wal_checkpoint(${mode})`);
+  return true;
+}
+
 function ensureProviderConnectionsColumns(db: SqliteDatabase) {
   try {
     const columns = db.prepare("PRAGMA table_info(provider_connections)").all() as Array<{
@@ -523,15 +530,39 @@ export function getDbInstance(): SqliteDatabase {
   return db;
 }
 
+export function closeDbInstance(options?: { checkpointMode?: CheckpointMode | null }): boolean {
+  const db = getDb();
+  if (!db) return false;
+
+  const checkpointMode = options?.checkpointMode ?? "TRUNCATE";
+
+  try {
+    if (checkpointMode) {
+      try {
+        if (checkpointDb(db, checkpointMode)) {
+          console.log(`[DB] SQLite WAL checkpoint completed (${checkpointMode}).`);
+        }
+      } catch (error: unknown) {
+        const message = error instanceof Error ? error.message : String(error);
+        console.warn(`[DB] WAL checkpoint failed during close (${checkpointMode}):`, message);
+      }
+    }
+  } finally {
+    try {
+      if (db.open) db.close();
+    } finally {
+      setDb(null);
+    }
+  }
+
+  return true;
+}
+
 /**
  * Reset the singleton (used by restore).
  */
 export function resetDbInstance() {
-  const db = getDb();
-  if (db) {
-    db.close();
-    setDb(null);
-  }
+  closeDbInstance();
 }
 
 // ──────────────── JSON → SQLite Migration ────────────────
diff --git a/src/lib/gracefulShutdown.ts b/src/lib/gracefulShutdown.ts
index 88291777..8bc09f5d 100644
--- a/src/lib/gracefulShutdown.ts
+++ b/src/lib/gracefulShutdown.ts
@@ -96,11 +96,9 @@ async function waitForDrain(): Promise<void> {
  */
 async function cleanup(): Promise<void> {
   try {
-    const { getDbInstance } = await import("@/lib/db/core");
-    const db = getDbInstance();
-    if (db && typeof db.close === "function") {
-      db.close();
-      console.log("[Shutdown] SQLite database closed.");
+    const { closeDbInstance } = await import("@/lib/db/core");
+    if (closeDbInstance()) {
+      console.log("[Shutdown] SQLite database checkpointed and closed.");
     }
   } catch (err) {
     console.error("[Shutdown] Error during cleanup:", (err as Error).message);
diff --git a/tests/unit/fixes-p1.test.mjs b/tests/unit/fixes-p1.test.mjs
index 636543b0..69e2c7e8 100644
--- a/tests/unit/fixes-p1.test.mjs
+++ b/tests/unit/fixes-p1.test.mjs
@@ -19,6 +19,8 @@ const proxyFetch = await import("../../open-sse/utils/proxyFetch.ts");
 const proxyDispatcher = await import("../../open-sse/utils/proxyDispatcher.ts");
 const proxySettingsRoute = await import("../../src/app/api/settings/proxy/route.ts");
 const proxyTestRoute = await import("../../src/app/api/settings/proxy/test/route.ts");
+const shutdownRoute = await import("../../src/app/api/shutdown/route.ts");
+const restartRoute = await import("../../src/app/api/restart/route.ts");
 
 async function withEnv(name, value, fn) {
   const previous = process.env[name];
@@ -141,6 +143,80 @@ test(
   }
 );
 
+test("closeDbInstance checkpoints WAL changes into the primary SQLite file", async () => {
+  await resetStorage();
+
+  const db = core.getDbInstance();
+  const now = new Date().toISOString();
+  db.prepare(
+    "INSERT INTO provider_connections (id, provider, auth_type, name, is_active, created_at, updated_at) VALUES (?, ?, ?, ?, ?, ?, ?)"
+  ).run("checkpoint-test-conn", "openai", "apikey", "checkpoint-test", 1, now, now);
+
+  core.closeDbInstance();
+
+  const snapshotPath = path.join(TEST_DATA_DIR, "storage-snapshot.sqlite");
+  fs.copyFileSync(core.SQLITE_FILE, snapshotPath);
+
+  const Database = (await import("better-sqlite3")).default;
+  const snapshotDb = new Database(snapshotPath, { readonly: true });
+  try {
+    const row = snapshotDb
+      .prepare("SELECT name FROM provider_connections WHERE id = ?")
+      .get("checkpoint-test-conn");
+    assert.equal(row?.name, "checkpoint-test");
+  } finally {
+    snapshotDb.close();
+  }
+});
+
+test("shutdown route uses SIGTERM for graceful shutdown", async () => {
+  const originalKill = process.kill;
+  const originalSetTimeout = globalThis.setTimeout;
+  const calls = [];
+
+  process.kill = (pid, signal) => {
+    calls.push({ pid, signal });
+    return true;
+  };
+  globalThis.setTimeout = (callback) => {
+    callback();
+    return 0;
+  };
+
+  try {
+    const response = await shutdownRoute.POST();
+    assert.equal(response.status, 200);
+    assert.deepEqual(calls, [{ pid: process.pid, signal: "SIGTERM" }]);
+  } finally {
+    process.kill = originalKill;
+    globalThis.setTimeout = originalSetTimeout;
+  }
+});
+
+test("restart route uses SIGTERM for graceful restart", async () => {
+  const originalKill = process.kill;
+  const originalSetTimeout = globalThis.setTimeout;
+  const calls = [];
+
+  process.kill = (pid, signal) => {
+    calls.push({ pid, signal });
+    return true;
+  };
+  globalThis.setTimeout = (callback) => {
+    callback();
+    return 0;
+  };
+
+  try {
+    const response = await restartRoute.POST();
+    assert.equal(response.status, 200);
+    assert.deepEqual(calls, [{ pid: process.pid, signal: "SIGTERM" }]);
+  } finally {
+    process.kill = originalKill;
+    globalThis.setTimeout = originalSetTimeout;
+  }
+});
+
 test("unlinkFileWithRetry retries EBUSY/EPERM and eventually succeeds", async () => {
   const target = path.join(TEST_DATA_DIR, "retry-target.tmp");
   fs.writeFileSync(target, "retry-me");