diff --git a/cmd/fix.go b/cmd/fix.go
index 523fafee..318a4de5 100644
--- a/cmd/fix.go
+++ b/cmd/fix.go
@@ -277,6 +277,23 @@ func fix(args []string, params *fixCommandParams) error {
 		ignore = params.ignoreFiles.v
 	}
 
+	// create a list of absolute paths, these will be used for the file from
+	// this point in order to be able to use the roots for format reporting.
+	absArgs := make([]string, len(args))
+
+	for i, arg := range args {
+		if filepath.IsAbs(arg) {
+			absArgs[i] = arg
+
+			continue
+		}
+
+		absArgs[i], err = filepath.Abs(arg)
+		if err != nil {
+			return fmt.Errorf("failed to get absolute path for %s: %w", arg, err)
+		}
+	}
+
 	filtered, err := config.FilterIgnoredPaths(args, ignore, true, "")
 	if err != nil {
 		return fmt.Errorf("failed to filter ignored paths: %w", err)
diff --git a/e2e/cli_test.go b/e2e/cli_test.go
index 80bd0158..d6715e47 100644
--- a/e2e/cli_test.go
+++ b/e2e/cli_test.go
@@ -779,6 +779,7 @@ func TestFix(t *testing.T) {
 	td := t.TempDir()
 
 	initialState := map[string]string{
+		".regal/config.yaml": "", // needed to find the root in the right place
 		"foo/main.rego": `package wow
 
 import rego.v1
@@ -821,13 +822,13 @@ test_allow {
 		mustWriteToFile(t, filepath.Join(td, file), string(content))
 	}
 
-	err := regal(&stdout, &stderr)("fix", td)
+	err := regal(&stdout, &stderr)("fix", filepath.Join(td, "foo"), filepath.Join(td, "bar"))
 
 	// 0 exit status is expected as all violations should have been fixed
 	expectExitCode(t, err, 0, &stdout, &stderr)
 
 	exp := fmt.Sprintf(`8 fixes applied:
-In project root: %s
+In project root: %[1]s
 bar/main.rego -> wow/foo-bar/baz/main.rego:
 - directory-package-mismatch
 
diff --git a/pkg/config/config.go b/pkg/config/config.go
index a2f409f1..d83968d4 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -675,22 +675,30 @@ func (rule *Rule) mapToConfig(result any) error {
 }
 
 func GetPotentialRoots(paths ...string) ([]string, error) {
+	var err error
+
 	dirMap := make(map[string]struct{})
 
-	for _, path := range paths {
-		abs, err := filepath.Abs(path)
-		if err != nil {
-			return nil, fmt.Errorf("failed to get absolute path for %s: %w", path, err)
+	absDirPaths := make([]string, len(paths))
+
+	for i, path := range paths {
+		abs := path
+
+		if !filepath.IsAbs(abs) {
+			abs, err = filepath.Abs(path)
+			if err != nil {
+				return nil, fmt.Errorf("failed to get absolute path for %s: %w", path, err)
+			}
 		}
 
 		if isDir(abs) {
-			dirMap[abs] = struct{}{}
+			absDirPaths[i] = abs
 		} else {
-			dirMap[filepath.Dir(abs)] = struct{}{}
+			absDirPaths[i] = filepath.Dir(abs)
 		}
 	}
 
-	for _, dir := range util.Keys(dirMap) {
+	for _, dir := range absDirPaths {
 		brds, err := FindBundleRootDirectories(dir)
 		if err != nil {
 			return nil, fmt.Errorf("failed to find bundle root directories in %s: %w", dir, err)
@@ -701,7 +709,12 @@ func GetPotentialRoots(paths ...string) ([]string, error) {
 		}
 	}
 
-	return util.Keys(dirMap), nil
+	foundRoots := util.Keys(dirMap)
+	if len(foundRoots) == 0 {
+		return absDirPaths, nil
+	}
+
+	return foundRoots, nil
 }
 
 func isDir(path string) bool {