diff --git a/internal/pkg/agent/application/upgrade/marker_access_common.go b/internal/pkg/agent/application/upgrade/marker_access_common.go
index d195577fa2d..aa7e1ccbf85 100644
--- a/internal/pkg/agent/application/upgrade/marker_access_common.go
+++ b/internal/pkg/agent/application/upgrade/marker_access_common.go
@@ -7,14 +7,25 @@ package upgrade
 import (
 	"fmt"
 	"os"
+	"path/filepath"
+	"sync"
+
+	"github.com/elastic/elastic-agent-libs/file"
 )
 
 func writeMarkerFileCommon(markerFile string, markerBytes []byte, shouldFsync bool) error {
-	f, err := os.OpenFile(markerFile, os.O_WRONLY|os.O_CREATE|os.O_TRUNC, 0600)
+	f, err := os.CreateTemp(
+		filepath.Dir(markerFile), fmt.Sprintf("%d-*.tmp", os.Getpid()))
 	if err != nil {
 		return fmt.Errorf("failed to open upgrade marker file for writing: %w", err)
 	}
-	defer f.Close()
+	once := sync.Once{}
+	closeFile := func() {
+		once.Do(func() {
+			f.Close()
+		})
+	}
+	defer closeFile()
 
 	if _, err := f.Write(markerBytes); err != nil {
 		return fmt.Errorf("failed to write upgrade marker file: %w", err)
@@ -27,6 +38,12 @@ func writeMarkerFileCommon(markerFile string, markerBytes []byte, shouldFsync bo
 	if err := f.Sync(); err != nil {
 		return fmt.Errorf("failed to sync upgrade marker file to disk: %w", err)
 	}
+	// I think we need to close before trying to swap the files on Windows
+	closeFile()
+
+	if err := file.SafeFileRotate(markerFile, f.Name()); err != nil {
+		return fmt.Errorf("failed to safe rotate upgrade marker file: %w", err)
+	}
 
 	return nil
 }
diff --git a/internal/pkg/agent/application/upgrade/marker_access_common_test.go b/internal/pkg/agent/application/upgrade/marker_access_common_test.go
deleted file mode 100644
index 5a599071794..00000000000
--- a/internal/pkg/agent/application/upgrade/marker_access_common_test.go
+++ /dev/null
@@ -1,56 +0,0 @@
-// Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
-// or more contributor license agreements. Licensed under the Elastic License;
-// you may not use this file except in compliance with the Elastic License.
-
-package upgrade
-
-import (
-	"math/rand"
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/stretchr/testify/require"
-)
-
-func TestWriteMarkerFileWithTruncation(t *testing.T) {
-	tmpDir := t.TempDir()
-	testMarkerFile := filepath.Join(tmpDir, markerFilename)
-
-	// Write a long marker file
-	err := writeMarkerFileCommon(testMarkerFile, randomBytes(40), true)
-	require.NoError(t, err)
-
-	// Get length of file
-	fileInfo, err := os.Stat(testMarkerFile)
-	require.NoError(t, err)
-	originalSize := fileInfo.Size()
-
-	// Write a shorter marker file
-	err = writeMarkerFileCommon(testMarkerFile, randomBytes(25), true)
-	require.NoError(t, err)
-
-	// Get length of file
-	fileInfo, err = os.Stat(testMarkerFile)
-	require.NoError(t, err)
-	newSize := fileInfo.Size()
-
-	// Make sure shorter file has is smaller in length than
-	// the original long marker file
-	require.Less(t, newSize, originalSize)
-}
-
-func randomBytes(length int) []byte {
-	chars := []rune("ABCDEFGHIJKLMNOPQRSTUVWXYZÅÄÖ" +
-		"abcdefghijklmnopqrstuvwxyzåäö" +
-		"0123456789" +
-		"~=+%^*/()[]{}/!@#$?|")
-
-	var b []byte
-	for i := 0; i < length; i++ {
-		rune := chars[rand.Intn(len(chars))]
-		b = append(b, byte(rune))
-	}
-
-	return b
-}
diff --git a/internal/pkg/agent/application/upgrade/marker_access_test.go b/internal/pkg/agent/application/upgrade/marker_access_test.go
index 3f1ff637eaa..6da55917c7a 100644
--- a/internal/pkg/agent/application/upgrade/marker_access_test.go
+++ b/internal/pkg/agent/application/upgrade/marker_access_test.go
@@ -5,10 +5,15 @@
 package upgrade
 
 import (
+	"context"
+	"errors"
+	"fmt"
+	"math/rand"
 	"os"
 	"path/filepath"
 	"testing"
 
+	"github.com/fsnotify/fsnotify"
 	"github.com/stretchr/testify/require"
 )
 
@@ -24,3 +29,121 @@ func TestWriteMarkerFile(t *testing.T) {
 	require.NoError(t, err)
 	require.Equal(t, markerBytes, data)
 }
+
+func TestWriteMarkerFileWithTruncation(t *testing.T) {
+	tmpDir := t.TempDir()
+	testMarkerFile := filepath.Join(tmpDir, markerFilename)
+
+	// Watch marker file for the duration of this test, to ensure
+	// it's never empty (truncated).
+	ctx, cancel := context.WithCancel(context.Background())
+	defer cancel()
+	errCh := make(chan error)
+	watchFileNotEmpty(t, ctx, testMarkerFile, errCh)
+	var watchErr error
+	go func() {
+		for {
+			select {
+			case <-ctx.Done():
+				return
+			case err := <-errCh:
+				watchErr = err
+			}
+		}
+	}()
+
+	// Write a long marker file
+	err := writeMarkerFile(testMarkerFile, randomBytes(40), true)
+	require.NoError(t, err, "could not write long marker file")
+
+	// Get length of file
+	fileInfo, err := os.Stat(testMarkerFile)
+	require.NoError(t, err)
+	originalSize := fileInfo.Size()
+
+	err = writeMarkerFile(testMarkerFile, randomBytes(25), true)
+	require.NoError(t, err)
+
+	// Get length of file
+	fileInfo, err = os.Stat(testMarkerFile)
+	require.NoError(t, err)
+	newSize := fileInfo.Size()
+
+	// Make sure shorter file is smaller than the original long marker file.
+	require.Less(t, newSize, originalSize)
+
+	// Cancel watch on marker file now that we're at the end of the test and
+	// check that there were no errors.
+	cancel()
+	require.NoError(t, watchErr)
+	close(errCh)
+}
+
+func watchFileNotEmpty(t *testing.T, ctx context.Context, filePath string, errCh chan error) {
+	watcher, err := fsnotify.NewWatcher()
+	require.NoError(t, err)
+
+	dirPath := filepath.Dir(filePath)
+	err = watcher.Add(dirPath)
+	require.NoError(t, err)
+
+	// Watch file
+	go func() {
+		defer watcher.Close()
+		for {
+			select {
+			case <-ctx.Done():
+				return
+			case err, ok := <-watcher.Errors:
+				if !ok { // Channel was closed (i.e. Watcher.Close() was called).
+					errCh <- errors.New("fsnotify.Watcher's error channel was closed")
+					return
+				}
+
+				errCh <- fmt.Errorf("upgrade marker watch returned error: %w", err)
+				continue
+			case e, ok := <-watcher.Events:
+				if !ok { // Channel was closed (i.e. Watcher.Close() was called).
+					errCh <- errors.New("fsnotify.Watcher's events channel was closed")
+					return
+				}
+
+				if e.Name != filePath {
+					// Since we are watching the directory that will contain the file, we
+					// could receive events here for changes to files other than the file we're
+					// interested in. We ignore such events.
+					continue
+				}
+
+				switch {
+				case e.Op&(fsnotify.Create|fsnotify.Write) != 0:
+					// File was created or updated; read its length
+					// and send error if it's zero
+					fileInfo, err := os.Stat(filePath)
+					if err != nil {
+						errCh <- fmt.Errorf("failed to stat file [%s]: %w", filePath, err)
+					}
+
+					if fileInfo.Size() == 0 {
+						errCh <- fmt.Errorf("file [%s] has size 0", filePath)
+					}
+				}
+			}
+		}
+	}()
+}
+
+func randomBytes(length int) []byte {
+	chars := []rune("ABCDEFGHIJKLMNOPQRSTUVWXYZÅÄÖ" +
+		"abcdefghijklmnopqrstuvwxyzåäö" +
+		"0123456789" +
+		"~=+%^*/()[]{}/!@#$?|")
+
+	var b []byte
+	for i := 0; i < length; i++ {
+		rune := chars[rand.Intn(len(chars))]
+		b = append(b, byte(rune))
+	}
+
+	return b
+}
diff --git a/internal/pkg/agent/application/upgrade/marker_access_windows.go b/internal/pkg/agent/application/upgrade/marker_access_windows.go
index cb37f9c0e88..15dfc61adc1 100644
--- a/internal/pkg/agent/application/upgrade/marker_access_windows.go
+++ b/internal/pkg/agent/application/upgrade/marker_access_windows.go
@@ -15,6 +15,7 @@ import (
 	"github.com/cenkalti/backoff/v4"
 )
 
+// TODO: is there an upper limit for this timeout?
 const markerAccessTimeout = 10 * time.Second
 const markerAccessBackoffInitialInterval = 50 * time.Millisecond
 const minMarkerAccessRetries = 5
@@ -71,6 +72,25 @@ func accessMarkerFileWithRetries(accessFn func() error) error {
 	defer cancel()
 
 	expBackoffWithTimeout := backoff.WithContext(expBackoff, ctx)
+	start := time.Now()
 
-	return backoff.Retry(accessFn, expBackoffWithTimeout)
+	var duration time.Duration
+	var count int
+	var err error
+	if err = accessFn(); err == nil {
+		return nil
+	}
+
+	for duration = expBackoffWithTimeout.NextBackOff(); duration != backoff.Stop; duration = expBackoffWithTimeout.NextBackOff() {
+		time.Sleep(duration)
+
+		if err = accessFn(); err == nil {
+			return nil
+		}
+
+		count++
+	}
+
+	return fmt.Errorf("could not write narker after %s and %d retries. Last error: %w",
+		time.Since(start), count, err)
 }