diff --git a/cmd/flux/bootstrap_github.go b/cmd/flux/bootstrap_github.go
index f85e1ec1..b9cf8450 100644
--- a/cmd/flux/bootstrap_github.go
+++ b/cmd/flux/bootstrap_github.go
@@ -23,6 +23,7 @@ import (
 	"net/url"
 	"os"
 	"path"
+	"path/filepath"
 	"time"
 
 	"github.com/spf13/cobra"
@@ -261,7 +262,7 @@ func bootstrapGitHubCmdRun(cmd *cobra.Command, args []string) error {
 
 	// configure repo synchronization
 	logger.Actionf("generating sync manifests")
-	syncManifests, err := generateSyncManifests(repoURL, bootstrapBranch, namespace, namespace, ghPath.String(), tmpDir, ghInterval)
+	syncManifests, err := generateSyncManifests(repoURL, bootstrapBranch, namespace, namespace, filepath.ToSlash(ghPath.String()), tmpDir, ghInterval)
 	if err != nil {
 		return err
 	}
diff --git a/cmd/flux/bootstrap_gitlab.go b/cmd/flux/bootstrap_gitlab.go
index 0ce55135..e8b9556c 100644
--- a/cmd/flux/bootstrap_gitlab.go
+++ b/cmd/flux/bootstrap_gitlab.go
@@ -23,6 +23,7 @@ import (
 	"net/url"
 	"os"
 	"path"
+	"path/filepath"
 	"regexp"
 	"time"
 
@@ -240,7 +241,7 @@ func bootstrapGitLabCmdRun(cmd *cobra.Command, args []string) error {
 
 	// configure repo synchronization
 	logger.Actionf("generating sync manifests")
-	syncManifests, err := generateSyncManifests(repoURL, bootstrapBranch, namespace, namespace, glPath.String(), tmpDir, glInterval)
+	syncManifests, err := generateSyncManifests(repoURL, bootstrapBranch, namespace, namespace, filepath.ToSlash(glPath.String()), tmpDir, glInterval)
 	if err != nil {
 		return err
 	}