diff --git a/api/krusty/kustomizer.go b/api/krusty/kustomizer.go
index 04919d747ff..0fd6e4aa104 100644
--- a/api/krusty/kustomizer.go
+++ b/api/krusty/kustomizer.go
@@ -5,6 +5,7 @@ package krusty
 
 import (
 	"fmt"
+	"log"
 
 	"sigs.k8s.io/kustomize/api/internal/builtins"
 	pLdr "sigs.k8s.io/kustomize/api/internal/plugins/loader"
@@ -18,6 +19,7 @@ import (
 	"sigs.k8s.io/kustomize/api/types"
 	"sigs.k8s.io/kustomize/kyaml/filesys"
 	"sigs.k8s.io/kustomize/kyaml/openapi"
+	"sigs.k8s.io/kustomize/kyaml/resid"
 )
 
 // Kustomizer performs kustomizations.
@@ -90,8 +92,33 @@ func (b *Kustomizer) Run(
 	if err != nil {
 		return nil, err
 	}
-	if b.options.DoLegacyResourceSort {
-		err = builtins.NewLegacyOrderTransformerPlugin().Transform(m)
+	// Sort order can be defined in two places:
+	// - (new) kustomization file
+	// - (old) CLI flag
+	//
+	// We want the kustomization file to take precedence over the CLI flag.
+	// Eventually, we may want to move away from having a CLI flag altogether:
+	// https://github.com/kubernetes-sigs/kustomize/issues/3947
+
+	// Case 1: Sort order set in kustomization file AND in CLI flag.
+	if b.options.SortModeSetExplicitly && kt.Kustomization().SortOptions != nil {
+		log.Println("Warning: Sorting order is set both in 'kustomization.yaml'" +
+			" ('sortOptions') and in a CLI flag ('--reorder'). Using the" +
+			" kustomization file over the CLI flag.")
+	}
+
+	// Case 2: Sort order set in CLI flag only or not at all.
+	if b.options.DoLegacyResourceSort && kt.Kustomization().SortOptions == nil {
+		pl := &builtins.SortOrderTransformerPlugin{
+			SortOptions: &types.SortOptions{
+				Order: types.LegacySortOrder,
+				LegacySortOptions: &types.LegacySortOptions{
+					OrderFirst: resid.OrderFirst,
+					OrderLast:  resid.OrderLast,
+				},
+			},
+		}
+		err = pl.Transform(m)
 		if err != nil {
 			return nil, err
 		}