diff --git a/command/check.go b/command/check.go
index e41f1aa81b..40753f2029 100644
--- a/command/check.go
+++ b/command/check.go
@@ -62,7 +62,7 @@ func (c *CheckCommand) Run(ctx context.Context, originalArgs []string) error {
 
 	fsys := os.DirFS(".")
 
-	files, err := loadYAMLFiles(fsys, args)
+	files, err := loadYAMLFiles(fsys, args, false)
 	if err != nil {
 		return err
 	}
diff --git a/command/command.go b/command/command.go
index 6c564ad2f1..8808e9ec9d 100644
--- a/command/command.go
+++ b/command/command.go
@@ -123,7 +123,7 @@ func (r loadResults) nodes() []*yaml.Node {
 	return n
 }
 
-func loadYAMLFiles(fsys fs.FS, paths []string) (loadResults, error) {
+func loadYAMLFiles(fsys fs.FS, paths []string, format bool) (loadResults, error) {
 	r := make(loadResults, 0, len(paths))
 
 	for _, pth := range paths {
@@ -137,12 +137,19 @@ func loadYAMLFiles(fsys fs.FS, paths []string) (loadResults, error) {
 		if err := yaml.Unmarshal(contents, &node); err != nil {
 			return nil, fmt.Errorf("failed to parse yaml for %s: %w", pth, err)
 		}
-
-		r = append(r, &loadResult{
+		lr := &loadResult{
 			path:     pth,
 			node:     &node,
 			contents: contents,
-		})
+		}
+
+		if format {
+			if err := FixIndentation(lr); err != nil {
+				return nil, fmt.Errorf("failed to format indentation: %w", err)
+			}
+		}
+
+		r = append(r, lr)
 	}
 
 	return r, nil
diff --git a/command/pin.go b/command/pin.go
index f6197cc2dc..de9b97cc84 100644
--- a/command/pin.go
+++ b/command/pin.go
@@ -80,7 +80,7 @@ func (c *PinCommand) Run(ctx context.Context, originalArgs []string) error {
 
 	fsys := os.DirFS(".")
 
-	files, err := loadYAMLFiles(fsys, args)
+	files, err := loadYAMLFiles(fsys, args, true)
 	if err != nil {
 		return err
 	}
@@ -89,10 +89,6 @@ func (c *PinCommand) Run(ctx context.Context, originalArgs []string) error {
 		return fmt.Errorf("-out must be a directory when pinning multiple files")
 	}
 
-	for _, f := range files {
-		FixIndentation(f)
-	}
-
 	if err := parser.Pin(ctx, res, par, files.nodes(), c.flagConcurrency); err != nil {
 		return fmt.Errorf("failed to pin refs: %w", err)
 	}
diff --git a/command/unpin.go b/command/unpin.go
index d307ec4044..b007dfd3ee 100644
--- a/command/unpin.go
+++ b/command/unpin.go
@@ -64,7 +64,7 @@ func (c *UnpinCommand) Run(ctx context.Context, originalArgs []string) error {
 
 	fsys := os.DirFS(".")
 
-	files, err := loadYAMLFiles(fsys, args)
+	files, err := loadYAMLFiles(fsys, args, true)
 	if err != nil {
 		return err
 	}
@@ -73,10 +73,6 @@ func (c *UnpinCommand) Run(ctx context.Context, originalArgs []string) error {
 		return fmt.Errorf("-out must be a directory when pinning multiple files")
 	}
 
-	for _, f := range files {
-		FixIndentation(f)
-	}
-
 	if err := parser.Unpin(ctx, files.nodes()); err != nil {
 		return fmt.Errorf("failed to pin refs: %w", err)
 	}
diff --git a/command/update.go b/command/update.go
index 9af7a1f166..e9f3a9060d 100644
--- a/command/update.go
+++ b/command/update.go
@@ -69,7 +69,7 @@ func (c *UpdateCommand) Run(ctx context.Context, originalArgs []string) error {
 
 	fsys := os.DirFS(".")
 
-	files, err := loadYAMLFiles(fsys, args)
+	files, err := loadYAMLFiles(fsys, args, true)
 	if err != nil {
 		return err
 	}
@@ -78,10 +78,6 @@ func (c *UpdateCommand) Run(ctx context.Context, originalArgs []string) error {
 		return fmt.Errorf("-out must be a directory when pinning multiple files")
 	}
 
-	for _, f := range files {
-		FixIndentation(f)
-	}
-
 	if err := parser.Unpin(ctx, files.nodes()); err != nil {
 		return fmt.Errorf("failed to pin refs: %w", err)
 	}
diff --git a/command/upgrade.go b/command/upgrade.go
index d0fba86d4a..edf308d6a0 100644
--- a/command/upgrade.go
+++ b/command/upgrade.go
@@ -77,7 +77,7 @@ func (c *UpgradeCommand) Run(ctx context.Context, originalArgs []string) error {
 
 	fsys := os.DirFS(".")
 
-	files, err := loadYAMLFiles(fsys, args)
+	files, err := loadYAMLFiles(fsys, args, true)
 	if err != nil {
 		return err
 	}
@@ -86,10 +86,6 @@ func (c *UpgradeCommand) Run(ctx context.Context, originalArgs []string) error {
 		return fmt.Errorf("-out must be a directory when upgrading multiple files")
 	}
 
-	for _, f := range files {
-		FixIndentation(f)
-	}
-
 	if err := parser.Unpin(ctx, files.nodes()); err != nil {
 		return fmt.Errorf("failed to unpin refs: %w", err)
 	}