diff --git a/apps/server/scripts/migrate-dev-db.ts b/apps/server/scripts/migrate-dev-db.ts
index 50d1b4e37909..38faef1f1cfd 100644
--- a/apps/server/scripts/migrate-dev-db.ts
+++ b/apps/server/scripts/migrate-dev-db.ts
@@ -210,6 +210,7 @@ const ensureNotInUse = Effect.fn("ensureDevDbNotInUse")(function* (databasePath:
   const checkpoint = yield* Effect.gen(function* () {
     const sql = yield* SqlClient.SqlClient;
     yield* sql.unsafe("PRAGMA busy_timeout = 0").unprepared;
+    yield* sql.unsafe("PRAGMA checkpoint_fullfsync = ON").unprepared;
     yield* sql.unsafe("BEGIN IMMEDIATE").unprepared;
     yield* sql.unsafe("ROLLBACK").unprepared;
     return yield* sql.unsafe<{ busy: number }>("PRAGMA wal_checkpoint(TRUNCATE)").unprepared;
@@ -483,6 +484,7 @@ export const runMigrateDevDb = Effect.fn("runMigrateDevDb")(function* (
     // WAL does not survive VACUUM INTO; set it so first `vp run dev` finds
     // the database exactly as server boot would have left it.
     yield* sql.unsafe("PRAGMA journal_mode = WAL").unprepared;
+    yield* sql.unsafe("PRAGMA checkpoint_fullfsync = ON").unprepared;
   }).pipe(
     Effect.provide(NodeSqliteClient.layer({ filename: databasePath })),
     wrapPhase("compact", databasePath),
diff --git a/apps/server/scripts/t3-sqlite-state.test.ts b/apps/server/scripts/t3-sqlite-state.test.ts
index fa5471bfa8c4..95936af3e1a2 100644
--- a/apps/server/scripts/t3-sqlite-state.test.ts
+++ b/apps/server/scripts/t3-sqlite-state.test.ts
@@ -72,6 +72,26 @@ it.layer(NodeServices.layer)("t3-sqlite-state", (it) => {
       if (result.operation === "query") {
         assert.deepStrictEqual(result.rows, [{ id: 1, label: "existing" }]);
       }
+
+      const checkpoint = yield* runSqliteState({
+        operation: "query",
+        baseDir,
+        sql: "PRAGMA checkpoint_fullfsync",
+      });
+      assert.equal(checkpoint.operation, "query");
+      if (checkpoint.operation === "query") {
+        assert.deepStrictEqual(checkpoint.rows, [{ checkpoint_fullfsync: 1 }]);
+      }
+
+      const fullfsync = yield* runSqliteState({
+        operation: "query",
+        baseDir,
+        sql: "PRAGMA fullfsync",
+      });
+      assert.equal(fullfsync.operation, "query");
+      if (fullfsync.operation === "query") {
+        assert.deepStrictEqual(fullfsync.rows, [{ fullfsync: 0 }]);
+      }
     }),
   );
 
diff --git a/apps/server/scripts/t3-sqlite-state.ts b/apps/server/scripts/t3-sqlite-state.ts
index 5e274588671f..a15d4994a4b3 100644
--- a/apps/server/scripts/t3-sqlite-state.ts
+++ b/apps/server/scripts/t3-sqlite-state.ts
@@ -201,6 +201,8 @@ export const runSqliteState = Effect.fn("runSqliteState")(function* (
   const program = Effect.gen(function* () {
     const sql = yield* SqlClient.SqlClient;
     yield* sql.unsafe("PRAGMA busy_timeout = 5000").unprepared;
+    // This connection bypasses Sqlite.ts and can checkpoint state.sqlite.
+    yield* sql.unsafe("PRAGMA checkpoint_fullfsync = ON").unprepared;
 
     if (input.operation === "query") {
       const rows = yield* sql.unsafe<RawSqliteRow>(source).unprepared.pipe(
diff --git a/apps/server/src/persistence/Layers/Sqlite.test.ts b/apps/server/src/persistence/Layers/Sqlite.test.ts
index 0b64e4f7fdcb..0518ebaa61f0 100644
--- a/apps/server/src/persistence/Layers/Sqlite.test.ts
+++ b/apps/server/src/persistence/Layers/Sqlite.test.ts
@@ -64,3 +64,15 @@ it.effect("applies busy_timeout in the shared persistence setup", () =>
     assert.equal(rows[0]?.timeout, 5000);
   }).pipe(Effect.provide(SqlitePersistenceMemory)),
 );
+
+it.effect("uses F_FULLFSYNC for WAL checkpoints and leaves per-commit fullfsync off", () =>
+  Effect.gen(function* () {
+    const sql = yield* SqlClient.SqlClient;
+    const checkpoint = yield* sql<{
+      readonly checkpoint_fullfsync: number;
+    }>`PRAGMA checkpoint_fullfsync`;
+    const fullfsync = yield* sql<{ readonly fullfsync: number }>`PRAGMA fullfsync`;
+    assert.equal(checkpoint[0]?.checkpoint_fullfsync, 1);
+    assert.equal(fullfsync[0]?.fullfsync, 0);
+  }).pipe(Effect.provide(SqlitePersistenceMemory)),
+);
diff --git a/apps/server/src/persistence/Layers/Sqlite.ts b/apps/server/src/persistence/Layers/Sqlite.ts
index 88342cbf1fad..e51e8f50becc 100644
--- a/apps/server/src/persistence/Layers/Sqlite.ts
+++ b/apps/server/src/persistence/Layers/Sqlite.ts
@@ -15,6 +15,9 @@ const setup = Layer.effectDiscard(
     yield* sql`PRAGMA busy_timeout = 5000;`;
     yield* sql`PRAGMA foreign_keys = ON;`;
     yield* sql`PRAGMA journal_mode = WAL;`;
+    // Checkpoint syncs use F_FULLFSYNC where the platform provides it. Ordinary
+    // commit sync stays on fsync(); PRAGMA fullfsync is left off.
+    yield* sql`PRAGMA checkpoint_fullfsync = ON;`;
     yield* runMigrations();
   }),
 );