diff --git a/cmds/portmaster-start/dirs.go b/cmds/portmaster-start/dirs.go
new file mode 100644
index 00000000..e327963f
--- /dev/null
+++ b/cmds/portmaster-start/dirs.go
@@ -0,0 +1,42 @@
+package main
+
+import (
+	"fmt"
+	"log"
+	"os"
+
+	"github.com/spf13/cobra"
+)
+
+func init() {
+	rootCmd.AddCommand(cleanStructureCmd)
+}
+
+var cleanStructureCmd = &cobra.Command{
+	Use:   "clean-structure",
+	Short: "Create and clean the required directory structure",
+	RunE: func(cmd *cobra.Command, args []string) error {
+		if err := ensureLoggingDir(); err != nil {
+			return err
+		}
+		return cleanAndEnsureExecDir()
+	},
+}
+
+func cleanAndEnsureExecDir() error {
+	execDir := dataRoot.ChildDir("exec", 0o777)
+
+	// Clean up and remove exec dir.
+	err := os.RemoveAll(execDir.Path)
+	if err != nil {
+		log.Printf("WARNING: failed to fully remove exec dir (%q) for cleaning: %s", execDir.Path, err)
+	}
+
+	// Re-create exec dir.
+	err = execDir.Ensure()
+	if err != nil {
+		return fmt.Errorf("failed to initialize exec dir (%q): %w", execDir.Path, err)
+	}
+
+	return nil
+}
diff --git a/cmds/portmaster-start/main.go b/cmds/portmaster-start/main.go
index 20f7a9f9..bd46cac8 100644
--- a/cmds/portmaster-start/main.go
+++ b/cmds/portmaster-start/main.go
@@ -51,7 +51,7 @@ var (
 				return err
 			}
 
-			if err := configureLogging(); err != nil {
+			if err := ensureLoggingDir(); err != nil {
 				return err
 			}
 
@@ -171,12 +171,12 @@ func configureRegistry(mustLoadIndex bool) error {
 	return updateRegistryIndex(mustLoadIndex)
 }
 
-func configureLogging() error {
+func ensureLoggingDir() error {
 	// set up logs root
 	logsRoot = dataRoot.ChildDir("logs", 0777)
 	err := logsRoot.Ensure()
 	if err != nil {
-		return fmt.Errorf("failed to initialize logs root: %s", err)
+		return fmt.Errorf("failed to initialize logs root (%q): %s", logsRoot.Path, err)
 	}
 
 	// warn about CTRL-C on windows