diff --git a/filebeat/beater/filebeat.go b/filebeat/beater/filebeat.go
index c3187fe60745..e09e24e66dfb 100644
--- a/filebeat/beater/filebeat.go
+++ b/filebeat/beater/filebeat.go
@@ -287,6 +287,7 @@ func (fb *Filebeat) Run(b *beat.Beat) error {
 	// Start the check-in loop, so Filebeat can respond to Elastic Agent,
 	// but it won't start any inputs/output
 	if err := b.Manager.PreInit(); err != nil {
+		fb.runReady.Close()
 		return err
 	}
 
diff --git a/filebeat/beater/stop_test.go b/filebeat/beater/stop_test.go
new file mode 100644
index 000000000000..72b3eb61bd82
--- /dev/null
+++ b/filebeat/beater/stop_test.go
@@ -0,0 +1,110 @@
+// Licensed to Elasticsearch B.V. under one or more contributor
+// license agreements. See the NOTICE file distributed with
+// this work for additional information regarding copyright
+// ownership. Elasticsearch B.V. licenses this file to you under
+// the Apache License, Version 2.0 (the "License"); you may
+// not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing,
+// software distributed under the License is distributed on an
+// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+// KIND, either express or implied.  See the License for the
+// specific language governing permissions and limitations
+// under the License.
+
+package beater
+
+import (
+	"errors"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/require"
+
+	"github.com/elastic/beats/v7/filebeat/fileset"
+	"github.com/elastic/beats/v7/libbeat/beat"
+	"github.com/elastic/beats/v7/libbeat/beatmonitoring"
+	"github.com/elastic/beats/v7/libbeat/management"
+	"github.com/elastic/elastic-agent-libs/logp"
+)
+
+// TestRunClosesRunReadyOnPreInitFailure guards against the regression in
+// commit 00068f7 where the defer fb.runReady.Close() was placed after the
+// PreInit call, leaving runReady unclosed when PreInit fails.  An unclosed
+// runReady causes StopWithContext to wait the full five-second timeout.
+func TestRunClosesRunReadyOnPreInitFailure(t *testing.T) {
+	preInitErr := errors.New("preinit failed")
+	fb := &Filebeat{
+		done:           make(chan struct{}),
+		runReady:       &closeOnce{ch: make(chan struct{})},
+		logger:         logp.NewNopLogger(),
+		moduleRegistry: new(fileset.ModuleRegistry),
+	}
+	b := &beat.Beat{
+		Info:       beat.Info{Logger: logp.NewNopLogger()},
+		Manager:    &preinitFailManager{err: preInitErr},
+		Monitoring: beatmonitoring.NewMonitoring(),
+	}
+
+	err := fb.Run(b)
+	require.ErrorIs(t, err, preInitErr)
+
+	select {
+	case <-fb.runReady.ch:
+		// runReady was closed — StopWithContext will not block
+	default:
+		t.Fatal("runReady was not closed after PreInit failure; StopWithContext would wait five seconds")
+	}
+}
+
+// preinitFailManager is a management.Manager stub whose PreInit returns an
+// error.  Only the methods called by Run before PreInit are implemented; any
+// other call panics, catching unexpected code paths during the test.
+type preinitFailManager struct {
+	management.Manager // zero-valued; panics on any unimplemented method
+	err                error
+}
+
+func (m *preinitFailManager) Enabled() bool  { return true }
+func (m *preinitFailManager) PreInit() error { return m.err }
+func (m *preinitFailManager) RegisterDiagnosticHook(_, _, _, _ string, _ management.DiagnosticHook) {
+}
+
+// TestStopWaitsForRunReady proves that Stop does not close the done channel
+// until Run has closed runReady (i.e., reached waitFinished.Wait).
+// This guards against a race where the OTel collector calls Shutdown before
+// the beat's Run goroutine has initialised its shutdown-signal machinery.
+func TestStopWaitsForRunReady(t *testing.T) {
+	fb := &Filebeat{
+		done:     make(chan struct{}),
+		runReady: &closeOnce{ch: make(chan struct{})},
+		logger:   logp.NewNopLogger(),
+	}
+
+	stopDone := make(chan struct{})
+	go func() {
+		defer close(stopDone)
+		fb.Stop()
+	}()
+
+	// done must still be open: Stop is waiting for runReady to be closed.
+	select {
+	case <-fb.done:
+		t.Fatal("Stop closed done before Run closed runReady")
+	default:
+	}
+
+	// Simulate Run() reaching the waitFinished.Wait() call.
+	fb.runReady.Close()
+
+	select {
+	case <-fb.done:
+	case <-time.After(500 * time.Millisecond):
+		t.Fatal("Stop did not close done after runReady was closed")
+	}
+
+	<-stopDone
+}