diff --git a/x-pack/elastic-agent/CHANGELOG.asciidoc b/x-pack/elastic-agent/CHANGELOG.asciidoc
index d0edf3666d5..4ceaff77f46 100644
--- a/x-pack/elastic-agent/CHANGELOG.asciidoc
+++ b/x-pack/elastic-agent/CHANGELOG.asciidoc
@@ -36,6 +36,7 @@
 - Windows agent doesn't uninstall with a lowercase `c:` drive in the path {pull}23998[23998]
 - Fix reloading of log level for services {pull}[24055]24055
 - Fix: Successfully installed and enrolled agent running standalone{pull}[24128]24128
+- Make installer atomic on windows {pull}[24253]24253
 
 ==== New features
 
diff --git a/x-pack/elastic-agent/pkg/agent/operation/operator.go b/x-pack/elastic-agent/pkg/agent/operation/operator.go
index a95bfe5b165..a0416545b11 100644
--- a/x-pack/elastic-agent/pkg/agent/operation/operator.go
+++ b/x-pack/elastic-agent/pkg/agent/operation/operator.go
@@ -36,6 +36,10 @@ const (
 	isMonitoringLogsFlag    = 1 << 1
 )
 
+type waiter interface {
+	Wait()
+}
+
 // Operator runs Start/Stop/Update operations
 // it is responsible for detecting reconnect to existing processes
 // based on backed up configuration
@@ -182,6 +186,13 @@ func (o *Operator) HandleConfig(cfg configrequest.Request) error {
 
 // Shutdown handles shutting down the running apps for Agent shutdown.
 func (o *Operator) Shutdown() {
+	//  wait for installer and downloader
+	if awaitable, ok := o.installer.(waiter); ok {
+		o.logger.Infof("waiting for installer of pipeline '%s' to finish", o.pipelineID)
+		awaitable.Wait()
+		o.logger.Debugf("pipeline installer '%s' done", o.pipelineID)
+	}
+
 	for _, app := range o.apps {
 		app.Shutdown()
 	}
diff --git a/x-pack/elastic-agent/pkg/artifact/install/atomic/atomic_installer.go b/x-pack/elastic-agent/pkg/artifact/install/atomic/atomic_installer.go
index f6c139ca463..980bb2127f9 100644
--- a/x-pack/elastic-agent/pkg/artifact/install/atomic/atomic_installer.go
+++ b/x-pack/elastic-agent/pkg/artifact/install/atomic/atomic_installer.go
@@ -9,6 +9,9 @@ import (
 	"io/ioutil"
 	"os"
 	"path/filepath"
+	"runtime"
+
+	"github.com/hashicorp/go-multierror"
 
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/agent/application/paths"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/agent/program"
@@ -51,15 +54,28 @@ func (i *Installer) Install(ctx context.Context, spec program.Spec, version, ins
 
 	if err := i.installer.Install(ctx, spec, version, tempInstallDir); err != nil {
 		// cleanup unfinished install
-		os.RemoveAll(tempInstallDir)
+		if rerr := os.RemoveAll(tempInstallDir); rerr != nil {
+			err = multierror.Append(err, rerr)
+		}
 		return err
 	}
 
 	if err := os.Rename(tempInstallDir, installDir); err != nil {
-		os.RemoveAll(installDir)
-		os.RemoveAll(tempInstallDir)
+		if rerr := os.RemoveAll(installDir); rerr != nil {
+			err = multierror.Append(err, rerr)
+		}
+		if rerr := os.RemoveAll(tempInstallDir); rerr != nil {
+			err = multierror.Append(err, rerr)
+		}
 		return err
 	}
 
+	// on windows rename is not atomic, let's force it to flush the cache
+	if runtime.GOOS == "windows" {
+		if f, err := os.OpenFile(installDir, os.O_SYNC|os.O_RDWR, 0755); err == nil {
+			f.Sync()
+		}
+	}
+
 	return nil
 }
diff --git a/x-pack/elastic-agent/pkg/artifact/install/awaitable/awaitable_installer.go b/x-pack/elastic-agent/pkg/artifact/install/awaitable/awaitable_installer.go
new file mode 100644
index 00000000000..3525def1c7f
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/artifact/install/awaitable/awaitable_installer.go
@@ -0,0 +1,57 @@
+// 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 awaitable
+
+import (
+	"context"
+	"sync"
+
+	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/agent/program"
+)
+
+type embeddedInstaller interface {
+	Install(ctx context.Context, spec program.Spec, version, installDir string) error
+}
+
+type embeddedChecker interface {
+	Check(ctx context.Context, spec program.Spec, version, installDir string) error
+}
+
+// Installer installs into temporary destination and moves to correct one after
+// successful finish.
+type Installer struct {
+	installer embeddedInstaller
+	checker   embeddedChecker
+	wg        sync.WaitGroup
+}
+
+// NewInstaller creates a new AtomicInstaller
+func NewInstaller(i embeddedInstaller, ch embeddedChecker) (*Installer, error) {
+	return &Installer{
+		installer: i,
+		checker:   ch,
+	}, nil
+}
+
+// Wait allows caller to wait for install to be finished
+func (i *Installer) Wait() {
+	i.wg.Wait()
+}
+
+// Install performs installation of program in a specific version.
+func (i *Installer) Install(ctx context.Context, spec program.Spec, version, installDir string) error {
+	i.wg.Add(1)
+	defer i.wg.Done()
+
+	return i.installer.Install(ctx, spec, version, installDir)
+}
+
+// Check performs installation checks
+func (i *Installer) Check(ctx context.Context, spec program.Spec, version, installDir string) error {
+	i.wg.Add(1)
+	defer i.wg.Done()
+
+	return i.checker.Check(ctx, spec, version, installDir)
+}
diff --git a/x-pack/elastic-agent/pkg/artifact/install/installer.go b/x-pack/elastic-agent/pkg/artifact/install/installer.go
index b99563ff997..a53cc46633b 100644
--- a/x-pack/elastic-agent/pkg/artifact/install/installer.go
+++ b/x-pack/elastic-agent/pkg/artifact/install/installer.go
@@ -12,6 +12,7 @@ import (
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/agent/program"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/artifact"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/artifact/install/atomic"
+	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/artifact/install/awaitable"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/artifact/install/dir"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/artifact/install/hooks"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/artifact/install/tar"
@@ -39,12 +40,20 @@ type InstallerChecker interface {
 	Check(ctx context.Context, spec program.Spec, version, installDir string) error
 }
 
+// AwaitableInstallerChecker is an interface that installs, checks but also is awaitable to check when actions are done.
+type AwaitableInstallerChecker interface {
+	InstallerChecker
+
+	// Waits for its work to be done.
+	Wait()
+}
+
 // NewInstaller returns a correct installer associated with a
 // package type:
 // - rpm -> rpm installer
 // - deb -> deb installer
 // - binary -> zip installer on windows, tar installer on linux and mac
-func NewInstaller(config *artifact.Config) (InstallerChecker, error) {
+func NewInstaller(config *artifact.Config) (AwaitableInstallerChecker, error) {
 	if config == nil {
 		return nil, ErrConfigNotProvided
 	}
@@ -66,5 +75,10 @@ func NewInstaller(config *artifact.Config) (InstallerChecker, error) {
 		return nil, err
 	}
 
-	return hooks.NewInstallerChecker(atomicInstaller, dir.NewChecker())
+	hooksInstaller, err := hooks.NewInstallerChecker(atomicInstaller, dir.NewChecker())
+	if err != nil {
+		return nil, err
+	}
+
+	return awaitable.NewInstaller(hooksInstaller, hooksInstaller)
 }
diff --git a/x-pack/elastic-agent/pkg/artifact/install/tar/tar_installer.go b/x-pack/elastic-agent/pkg/artifact/install/tar/tar_installer.go
index 2452f5909cc..421a30bed4f 100644
--- a/x-pack/elastic-agent/pkg/artifact/install/tar/tar_installer.go
+++ b/x-pack/elastic-agent/pkg/artifact/install/tar/tar_installer.go
@@ -33,7 +33,7 @@ func NewInstaller(config *artifact.Config) (*Installer, error) {
 
 // Install performs installation of program in a specific version.
 // It expects package to be already downloaded.
-func (i *Installer) Install(_ context.Context, spec program.Spec, version, installDir string) error {
+func (i *Installer) Install(ctx context.Context, spec program.Spec, version, installDir string) error {
 	artifactPath, err := artifact.GetArtifactPath(spec, version, i.config.OS(), i.config.Arch(), i.config.TargetDirectory)
 	if err != nil {
 		return err
@@ -53,10 +53,10 @@ func (i *Installer) Install(_ context.Context, spec program.Spec, version, insta
 
 	// unpack must occur in directory that holds the installation directory
 	// or the extraction will be double nested
-	return unpack(f, filepath.Dir(installDir))
+	return unpack(ctx, f, filepath.Dir(installDir))
 }
 
-func unpack(r io.Reader, dir string) error {
+func unpack(ctx context.Context, r io.Reader, dir string) error {
 	zr, err := gzip.NewReader(r)
 	if err != nil {
 		return errors.New("requires gzip-compressed body", err, errors.TypeFilesystem)
@@ -66,6 +66,11 @@ func unpack(r io.Reader, dir string) error {
 	var rootDir string
 
 	for {
+		// exit and propagate cancellation err as soon as we know about it
+		if err := ctx.Err(); err != nil {
+			return err
+		}
+
 		f, err := tr.Next()
 		if err == io.EOF {
 			break
diff --git a/x-pack/elastic-agent/pkg/artifact/install/zip/zip_installer.go b/x-pack/elastic-agent/pkg/artifact/install/zip/zip_installer.go
index fdd374eb72a..3073da25ca4 100644
--- a/x-pack/elastic-agent/pkg/artifact/install/zip/zip_installer.go
+++ b/x-pack/elastic-agent/pkg/artifact/install/zip/zip_installer.go
@@ -37,7 +37,7 @@ func NewInstaller(config *artifact.Config) (*Installer, error) {
 
 // Install performs installation of program in a specific version.
 // It expects package to be already downloaded.
-func (i *Installer) Install(_ context.Context, spec program.Spec, version, installDir string) error {
+func (i *Installer) Install(ctx context.Context, spec program.Spec, version, installDir string) error {
 	artifactPath, err := artifact.GetArtifactPath(spec, version, i.config.OS(), i.config.Arch(), i.config.TargetDirectory)
 	if err != nil {
 		return err
@@ -49,7 +49,7 @@ func (i *Installer) Install(_ context.Context, spec program.Spec, version, insta
 		os.RemoveAll(installDir)
 	}
 
-	if err := i.unzip(artifactPath); err != nil {
+	if err := i.unzip(ctx, artifactPath); err != nil {
 		return err
 	}
 
@@ -69,7 +69,7 @@ func (i *Installer) Install(_ context.Context, spec program.Spec, version, insta
 	return nil
 }
 
-func (i *Installer) unzip(artifactPath string) error {
+func (i *Installer) unzip(ctx context.Context, artifactPath string) error {
 	r, err := zip.OpenReader(artifactPath)
 	if err != nil {
 		return err
@@ -120,6 +120,11 @@ func (i *Installer) unzip(artifactPath string) error {
 	}
 
 	for _, f := range r.File {
+		// if we were cancelled in between
+		if err := ctx.Err(); err != nil {
+			return err
+		}
+
 		if err := unpackFile(f); err != nil {
 			return err
 		}