diff --git a/dify-agent-runtime/Makefile b/dify-agent-runtime/Makefile
index 533248f5e1d..3cbe4d54b07 100644
--- a/dify-agent-runtime/Makefile
+++ b/dify-agent-runtime/Makefile
@@ -143,3 +143,6 @@ sync-e2b-template-dev:
 
 sync-e2b-template-prod:
 	E2B_API_KEY=$(E2B_API_KEY_PROD) ./docker/sync-e2b-template.sh
+
+benchmark:
+	go test ./benchmarks/ -bench . -run '^$$' -benchtime 40x
diff --git a/dify-agent-runtime/benchmarks/e2e_test.go b/dify-agent-runtime/benchmarks/e2e_test.go
new file mode 100644
index 00000000000..5b1ab4dd392
--- /dev/null
+++ b/dify-agent-runtime/benchmarks/e2e_test.go
@@ -0,0 +1,212 @@
+// End-to-end benchmarks that drive the real shellctl HTTP API in-process.
+//
+// Unlike perf_test.go (which isolates single techniques), this boots an actual
+// *server.Service + Handler over httptest and fires real POST /v1/jobs/run
+// requests, so it exercises the full path: job-dir mkdir, script/env writes,
+// SQLite commits, tmux fork/exec, the WaitJob poll loop, and the background
+// pipe monitor. It only uses stable exported APIs so it compiles unchanged
+// against both the optimized and pre-optimization ("git stash") server code.
+//
+// Because it lives in an untracked file, `git stash` does NOT remove it — so
+// the before/after workflow is:
+//
+//	go test ./benchmarks/ -bench E2E -run '^$' -benchtime 200x | tee after.txt
+//	git stash
+//	go test ./benchmarks/ -bench E2E -run '^$' -benchtime 200x | tee before.txt
+//	git stash pop
+//	benchstat before.txt after.txt   # optional
+//
+// Requires tmux on PATH. The shellctl helper binaries are built automatically
+// into a temp dir the first time a benchmark runs.
+package benchmarks
+
+import (
+	"bytes"
+	"encoding/json"
+	"fmt"
+	"io"
+	"log"
+	"net/http"
+	"net/http/httptest"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"sync"
+	"testing"
+
+	"github.com/langgenius/dify/dify-agent-runtime/internal/server"
+)
+
+const modulePath = "github.com/langgenius/dify/dify-agent-runtime"
+
+var (
+	buildOnce sync.Once
+	buildErr  error
+	binDir    string
+)
+
+// ensureBinaries builds the shellctl helper binaries the server shells out to
+// (runner, sanitize-pty, runner-exit) once per test process and prepends their
+// directory to PATH so both installRunner's LookPath and the tmux-invoked
+// sanitize/runner-exit commands resolve.
+func ensureBinaries(tb testing.TB) {
+	tb.Helper()
+	buildOnce.Do(func() {
+		// Silence the server's request/lifecycle logging so it neither skews
+		// timings with I/O nor interleaves with benchmark output.
+		log.SetOutput(io.Discard)
+		if _, err := exec.LookPath("tmux"); err != nil {
+			buildErr = fmt.Errorf("tmux not found in PATH")
+			return
+		}
+		dir, err := os.MkdirTemp("/tmp", "agbench-bin")
+		if err != nil {
+			buildErr = err
+			return
+		}
+		binDir = dir
+		targets := map[string]string{
+			"shellctl-runner":       modulePath + "/cmd/runner",
+			"shellctl-sanitize-pty": modulePath + "/cmd/sanitize-pty",
+			"shellctl-runner-exit":  modulePath + "/cmd/runner-exit",
+		}
+		for name, pkg := range targets {
+			out := filepath.Join(dir, name)
+			cmd := exec.Command("go", "build", "-o", out, pkg)
+			if b, err := cmd.CombinedOutput(); err != nil {
+				buildErr = fmt.Errorf("build %s: %v: %s", name, err, b)
+				return
+			}
+		}
+		_ = os.Setenv("PATH", binDir+string(os.PathListSeparator)+os.Getenv("PATH"))
+	})
+	if buildErr != nil {
+		tb.Skipf("cannot build shellctl binaries: %v", buildErr)
+	}
+}
+
+// startServer boots a fresh in-process shellctl server with background GC and
+// the pipe monitor running (matching production wiring). Returns the base URL,
+// auth token, and a cleanup func.
+func startServer(tb testing.TB) (string, string, func()) {
+	tb.Helper()
+	ensureBinaries(tb)
+
+	stateDir, err := os.MkdirTemp("/tmp", "agbench-state")
+	if err != nil {
+		tb.Fatalf("mkdtemp state: %v", err)
+	}
+	cwd, err := os.MkdirTemp("/tmp", "agbench-cwd")
+	if err != nil {
+		tb.Fatalf("mkdtemp cwd: %v", err)
+	}
+
+	cfg, err := server.DefaultConfig()
+	if err != nil {
+		tb.Fatalf("default config: %v", err)
+	}
+	cfg.StateDir = stateDir
+	cfg.RuntimeDir = filepath.Join(stateDir, "runtime")
+	cfg.DefaultCwd = cwd
+	cfg.AuthToken = "bench-token"
+
+	svc := server.NewService(cfg)
+	if err := svc.Initialize(); err != nil {
+		tb.Fatalf("service initialize: %v", err)
+	}
+	svc.StartBackgroundGC()
+	svc.StartBackgroundPipeMonitor()
+
+	ts := httptest.NewServer(server.Handler(svc, cfg))
+
+	cleanup := func() {
+		ts.Close()
+		svc.Shutdown()
+		// Kill the dedicated tmux server so background sleep jobs don't leak.
+		kill := exec.Command("tmux", "-S", cfg.TmuxSocket(), "kill-server")
+		_ = kill.Run()
+		_ = os.RemoveAll(stateDir)
+		_ = os.RemoveAll(cwd)
+	}
+	return ts.URL, cfg.AuthToken, cleanup
+}
+
+func runJob(tb testing.TB, client *http.Client, baseURL, token, script string, timeout float64) {
+	tb.Helper()
+	payload, _ := json.Marshal(map[string]any{"script": script, "timeout": timeout})
+	req, _ := http.NewRequest("POST", baseURL+"/v1/jobs/run", bytes.NewReader(payload))
+	req.Header.Set("Content-Type", "application/json")
+	req.Header.Set("Authorization", "Bearer "+token)
+	resp, err := client.Do(req)
+	if err != nil {
+		tb.Fatalf("run job: %v", err)
+	}
+	_, _ = io.Copy(io.Discard, resp.Body)
+	_ = resp.Body.Close()
+	if resp.StatusCode != 200 {
+		tb.Fatalf("run job status = %d", resp.StatusCode)
+	}
+}
+
+// BenchmarkE2E_RunEcho measures full request latency for a trivial job that
+// creates, starts, runs, and completes: the RunJob write path (3 SQLite
+// commits) plus the WaitJob poll loop's per-poll runtime-state tmux calls.
+func BenchmarkE2E_RunEcho(b *testing.B) {
+	baseURL, token, cleanup := startServer(b)
+	defer cleanup()
+	client := &http.Client{}
+
+	// Prime tmux/server lazy init.
+	runJob(b, client, baseURL, token, "echo warmup", 5)
+
+	b.ResetTimer()
+	for b.Loop() {
+		runJob(b, client, baseURL, token, "echo hi", 5)
+	}
+}
+
+// BenchmarkE2E_RunEchoParallel drives many concurrent run requests. This is
+// where the optimizations bite: the single-writer SQLite connection serializes
+// commits (so per-commit fsync cost is on the critical path) and concurrent
+// tmux fork/exec competes for CPU, so halving forks + dropping fsync raises
+// sustained throughput even though single-request latency is gated by fixed
+// poll/handshake waits.
+func BenchmarkE2E_RunEchoParallel(b *testing.B) {
+	baseURL, token, cleanup := startServer(b)
+	defer cleanup()
+
+	runJob(b, &http.Client{}, baseURL, token, "echo warmup", 5)
+
+	b.ResetTimer()
+	b.RunParallel(func(pb *testing.PB) {
+		client := &http.Client{}
+		for pb.Next() {
+			runJob(b, client, baseURL, token, "echo hi", 5)
+		}
+	})
+}
+
+// BenchmarkE2E_RunEchoUnderMonitorLoad keeps N long-running jobs alive so the
+// 1s background pipe monitor reconciles them every tick (2N tmux forks before,
+// 1 after), then measures echo-job latency under that contention on the shared
+// single-writer SQLite connection and CPU.
+func BenchmarkE2E_RunEchoUnderMonitorLoad(b *testing.B) {
+	for _, n := range []int{8, 32} {
+		b.Run(fmt.Sprintf("running=%d", n), func(b *testing.B) {
+			baseURL, token, cleanup := startServer(b)
+			defer cleanup()
+			client := &http.Client{}
+
+			// Seed N background jobs: sleep long, but return the run call
+			// quickly via a short wait timeout so the job stays running.
+			for i := 0; i < n; i++ {
+				runJob(b, client, baseURL, token, "sleep 600", 0.3)
+			}
+
+			b.ResetTimer()
+			for b.Loop() {
+				runJob(b, client, baseURL, token, "echo hi", 5)
+			}
+		})
+	}
+}
diff --git a/dify-agent-runtime/cmd/runner/main.go b/dify-agent-runtime/cmd/runner/main.go
index 9d9a669f885..945a20f01ed 100644
--- a/dify-agent-runtime/cmd/runner/main.go
+++ b/dify-agent-runtime/cmd/runner/main.go
@@ -33,6 +33,12 @@ import (
 	"github.com/langgenius/dify/dify-agent-runtime/internal/landlock"
 )
 
+// startGatePollInterval is how often the parent runner checks for the
+// start-gate handshake file. It is a cheap local stat on the same path the
+// server has just written, so a fine interval keeps per-job startup latency
+// low without meaningful cost.
+const startGatePollInterval = 5 * time.Millisecond
+
 func main() {
 	if len(os.Args) > 1 && os.Args[1] == "--exec" {
 		childMode()
@@ -67,7 +73,7 @@ func parentMode() {
 		if _, err := os.Stat(startGate); err == nil {
 			break
 		}
-		time.Sleep(50 * time.Millisecond)
+		time.Sleep(startGatePollInterval)
 	}
 
 	// Load environment overlay from JSON.
diff --git a/dify-agent-runtime/internal/server/config.go b/dify-agent-runtime/internal/server/config.go
index a329bd512f4..c30ed34df70 100644
--- a/dify-agent-runtime/internal/server/config.go
+++ b/dify-agent-runtime/internal/server/config.go
@@ -23,7 +23,7 @@ const (
 	DefaultTerminateGraceSeconds         = 10.0
 	DefaultGCIntervalSeconds             = 60.0
 	DefaultGCFinishedJobRetentionSeconds = 300.0
-	DefaultPollInterval                  = 50 * time.Millisecond
+	DefaultPollInterval                  = 5 * time.Millisecond
 	DefaultPipeMonitorInterval           = 1 * time.Second
 	DefaultPipeReadyTimeout              = 10 * time.Second
 	DefaultSQLiteBusyTimeoutMs           = 5000
diff --git a/dify-agent-runtime/internal/server/db.go b/dify-agent-runtime/internal/server/db.go
index e6353e77e97..e64c01cbaf9 100644
--- a/dify-agent-runtime/internal/server/db.go
+++ b/dify-agent-runtime/internal/server/db.go
@@ -68,7 +68,14 @@ type DB struct {
 
 // OpenDB opens (or creates) the shellctl SQLite database.
 func OpenDB(dbPath string, busyTimeoutMs int) (*DB, error) {
-	dsn := fmt.Sprintf("file:%s?_pragma=busy_timeout(%d)&_pragma=journal_mode(WAL)", dbPath, busyTimeoutMs)
+	// synchronous=NORMAL is durable and crash-safe under WAL: it only fsyncs on
+	// checkpoint rather than on every commit, which removes the per-write fsync
+	// on the job-creation path. Worst case on power loss is losing the last few
+	// transactions of ephemeral job state, never DB corruption.
+	dsn := fmt.Sprintf(
+		"file:%s?_pragma=busy_timeout(%d)&_pragma=journal_mode(WAL)&_pragma=synchronous(NORMAL)",
+		dbPath, busyTimeoutMs,
+	)
 	db, err := sql.Open("sqlite", dsn)
 	if err != nil {
 		return nil, fmt.Errorf("open sqlite: %w", err)