diff --git a/pkg/fleet/installer/service/datadog_agent_windows.go b/pkg/fleet/installer/service/datadog_agent_windows.go
index 5b5b9097cb56f..35284e0bb2351 100644
--- a/pkg/fleet/installer/service/datadog_agent_windows.go
+++ b/pkg/fleet/installer/service/datadog_agent_windows.go
@@ -31,7 +31,7 @@ func SetupAgent(ctx context.Context, args []string) (err error) {
 		span.Finish(tracer.WithError(err))
 	}()
 	// Make sure there are no Agent already installed
-	_ = removeProduct("Datadog Agent")
+	_ = removeAgentIfInstalled(ctx)
 	err = installAgentPackage("stable", args)
 	return err
 }
@@ -91,17 +91,10 @@ func PromoteAgentExperiment(_ context.Context) error {
 
 // RemoveAgent stops and removes the agent
 func RemoveAgent(ctx context.Context) (err error) {
-	span, _ := tracer.StartSpanFromContext(ctx, "remove_agent")
-	defer func() {
-		if err != nil {
-			// removal failed, this should rarely happen.
-			// Rollback might have restored the Agent, but we can't be sure.
-			log.Errorf("Failed to remove agent: %s", err)
-		}
-		span.Finish(tracer.WithError(err))
-	}()
-	err = removeProduct("Datadog Agent")
-	return err
+	// Don't return an error if the Agent is already not installed.
+	// returning an error here will prevent the package from being removed
+	// from the local repository.
+	return removeAgentIfInstalled(ctx)
 }
 
 // ConfigureAgent noop
@@ -118,9 +111,18 @@ func installAgentPackage(target string, args []string) error {
 	return nil
 }
 
-func removeAgentIfInstalled(ctx context.Context) error {
+func removeAgentIfInstalled(ctx context.Context) (err error) {
 	if isProductInstalled("Datadog Agent") {
-		err := RemoveAgent(ctx)
+		span, _ := tracer.StartSpanFromContext(ctx, "remove_agent")
+		defer func() {
+			if err != nil {
+				// removal failed, this should rarely happen.
+				// Rollback might have restored the Agent, but we can't be sure.
+				log.Errorf("Failed to remove agent: %s", err)
+			}
+			span.Finish(tracer.WithError(err))
+		}()
+		err := removeProduct("Datadog Agent")
 		if err != nil {
 			return err
 		}
diff --git a/test/new-e2e/tests/installer/windows/base_suite.go b/test/new-e2e/tests/installer/windows/base_suite.go
index 5a3fd22833af5..cde5d2be78610 100644
--- a/test/new-e2e/tests/installer/windows/base_suite.go
+++ b/test/new-e2e/tests/installer/windows/base_suite.go
@@ -61,6 +61,7 @@ type BaseInstallerSuite struct {
 	currentAgentVersion    agentVersion.Version
 	stableInstallerVersion PackageVersion
 	stableAgentVersion     PackageVersion
+	outputDir              string
 }
 
 // Installer the Datadog Installer for testing.
@@ -115,10 +116,11 @@ func (s *BaseInstallerSuite) SetupSuite() {
 func (s *BaseInstallerSuite) BeforeTest(suiteName, testName string) {
 	s.BaseSuite.BeforeTest(suiteName, testName)
 
-	outputDir, err := runner.GetTestOutputDir(runner.GetProfile(), s.T())
+	var err error
+	s.outputDir, err = runner.GetTestOutputDir(runner.GetProfile(), s.T())
 	s.Require().NoError(err, "should get output dir")
-	s.T().Logf("Output dir: %s", outputDir)
-	s.installer = NewDatadogInstaller(s.Env(), outputDir)
+	s.T().Logf("Output dir: %s", s.outputDir)
+	s.installer = NewDatadogInstaller(s.Env(), s.outputDir)
 }
 
 // Require instantiates a suiteAssertions for the current suite.
@@ -132,3 +134,8 @@ func (s *BaseInstallerSuite) BeforeTest(suiteName, testName string) {
 func (s *BaseInstallerSuite) Require() *suiteasserts.SuiteAssertions {
 	return suiteasserts.New(s.BaseSuite.Require(), s)
 }
+
+// OutputDir returns the output directory for the test
+func (s *BaseInstallerSuite) OutputDir() string {
+	return s.outputDir
+}
diff --git a/test/new-e2e/tests/installer/windows/suites/agent-package/install_test.go b/test/new-e2e/tests/installer/windows/suites/agent-package/install_test.go
index b318186b53f72..38fd858783940 100644
--- a/test/new-e2e/tests/installer/windows/suites/agent-package/install_test.go
+++ b/test/new-e2e/tests/installer/windows/suites/agent-package/install_test.go
@@ -7,9 +7,13 @@
 package agenttests
 
 import (
+	"path/filepath"
+
 	"github.com/DataDog/datadog-agent/test/new-e2e/pkg/e2e"
 	"github.com/DataDog/datadog-agent/test/new-e2e/pkg/environments/aws/host/windows"
 	installerwindows "github.com/DataDog/datadog-agent/test/new-e2e/tests/installer/windows"
+	windowsAgent "github.com/DataDog/datadog-agent/test/new-e2e/tests/windows/common/agent"
+
 	"testing"
 )
 
@@ -30,7 +34,7 @@ func TestAgentInstalls(t *testing.T) {
 func (s *testAgentInstallSuite) TestInstallAgentPackage() {
 	s.Run("Install", func() {
 		s.installAgent()
-		s.Run("Uninstall", s.uninstallAgent)
+		s.Run("Uninstall", s.removeAgentPackage)
 	})
 }
 
@@ -45,7 +49,7 @@ func (s *testAgentInstallSuite) installAgent() {
 	s.Require().Host(s.Env().RemoteHost).HasARunningDatadogAgentService()
 }
 
-func (s *testAgentInstallSuite) uninstallAgent() {
+func (s *testAgentInstallSuite) removeAgentPackage() {
 	// Arrange
 
 	// Act
@@ -54,4 +58,33 @@ func (s *testAgentInstallSuite) uninstallAgent() {
 	// Assert
 	s.Require().NoErrorf(err, "failed to remove the Datadog Agent package: %s", output)
 	s.Require().Host(s.Env().RemoteHost).HasNoDatadogAgentService()
+	s.Require().Host(s.Env().RemoteHost).
+		NoDirExists(installerwindows.GetStableDirFor(installerwindows.AgentPackage),
+			"the package directory should be removed")
+}
+
+func (s *testAgentInstallSuite) TestRemoveAgentAfterMSIUninstall() {
+	// Arrange
+	s.installAgent()
+	s.uninstallAgentWithMSI()
+
+	// Act
+
+	// Assert
+	s.removeAgentPackage()
+}
+
+func (s *testAgentInstallSuite) uninstallAgentWithMSI() {
+	// Arrange
+
+	// Act
+	err := windowsAgent.UninstallAgent(s.Env().RemoteHost,
+		filepath.Join(s.OutputDir(), "uninstall.log"),
+	)
+
+	// Assert
+	s.Require().NoErrorf(err, "failed to uninstall the Datadog Agent package")
+	s.Require().Host(s.Env().RemoteHost).
+		DirExists(installerwindows.GetStableDirFor(installerwindows.AgentPackage),
+			"the package directory should still exist after manually uninstalling the Agent with the MSI")
 }