diff --git a/bundle/config/mutator/prepend_workspace_prefix.go b/bundle/config/mutator/prepend_workspace_prefix.go
index de71bf7f..e0be2572 100644
--- a/bundle/config/mutator/prepend_workspace_prefix.go
+++ b/bundle/config/mutator/prepend_workspace_prefix.go
@@ -44,6 +44,11 @@ func (m *prependWorkspacePrefix) Apply(ctx context.Context, b *bundle.Bundle) di
 					return dyn.InvalidValue, fmt.Errorf("expected string, got %s", v.Kind())
 				}
 
+				// Skip prefixing if the path does not start with /, it might be variable reference or smth else.
+				if !strings.HasPrefix(path, "/") {
+					return pv, nil
+				}
+
 				for _, prefix := range skipPrefixes {
 					if strings.HasPrefix(path, prefix) {
 						return pv, nil
diff --git a/bundle/config/mutator/prepend_workspace_prefix_test.go b/bundle/config/mutator/prepend_workspace_prefix_test.go
index 6fbadec5..31393e6b 100644
--- a/bundle/config/mutator/prepend_workspace_prefix_test.go
+++ b/bundle/config/mutator/prepend_workspace_prefix_test.go
@@ -31,6 +31,14 @@ func TestPrependWorkspacePrefix(t *testing.T) {
 			path:     "/Volumes/Users/test",
 			expected: "/Volumes/Users/test",
 		},
+		{
+			path:     "~/test",
+			expected: "~/test",
+		},
+		{
+			path:     "${workspace.file_path}/test",
+			expected: "${workspace.file_path}/test",
+		},
 	}
 
 	for _, tc := range testCases {