diff --git a/api/krusty/kustomizer.go b/api/krusty/kustomizer.go
index 8de435360f9..94962abd207 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"
@@ -90,8 +91,37 @@ 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.
+	if kt.Kustomization().SortOptions != nil {
+		// If set in CLI flag too, warn the user.
+		if b.options.Reorder != ReorderOptionUnspecified {
+			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.")
+		}
+		pl := &builtins.SortOrderTransformerPlugin{
+			SortOptions: kt.Kustomization().SortOptions,
+		}
+		err = pl.Transform(m)
+		if err != nil {
+			return nil, err
+		}
+	} else if b.options.Reorder == ReorderOptionLegacy || b.options.Reorder == ReorderOptionUnspecified {
+		// Case 2: Sort order set in CLI flag only or not at all.
+		pl := &builtins.SortOrderTransformerPlugin{
+			SortOptions: &types.SortOptions{
+				Order: types.LegacySortOrder,
+			},
+		}
+		err = pl.Transform(m)
 		if err != nil {
 			return nil, err
 		}
diff --git a/kustomize/commands/build/reorderoutput.go b/kustomize/commands/build/reorderoutput.go
index c0495bedc0c..3ff3dadff0e 100644
--- a/kustomize/commands/build/reorderoutput.go
+++ b/kustomize/commands/build/reorderoutput.go
@@ -7,6 +7,7 @@ import (
 	"fmt"
 
 	"github.com/spf13/pflag"
+	"sigs.k8s.io/kustomize/api/krusty"
 )
 
 //go:generate stringer -type=reorderOutput
@@ -23,32 +24,31 @@ const flagReorderOutputName = "reorder"
 func AddFlagReorderOutput(set *pflag.FlagSet) {
 	set.StringVar(
 		&theFlags.reorderOutput, flagReorderOutputName,
-		legacy.String(),
-		"Reorder the resources just before output. "+
-			"Use '"+legacy.String()+"' to apply a legacy reordering "+
-			"(Namespaces first, Webhooks last, etc). "+
-			"Use '"+none.String()+"' to suppress a final reordering.")
+		unspecified.String(),
+		"Reorder the resources just before output. Use '"+legacy.String()+"' to"+
+			" apply a legacy reordering (Namespaces first, Webhooks last, etc)."+
+			" Use '"+none.String()+"' to suppress a final reordering.")
 }
 
 func validateFlagReorderOutput() error {
 	switch theFlags.reorderOutput {
-	case none.String(), legacy.String():
+	case none.String(), legacy.String(), unspecified.String():
 		return nil
 	default:
 		return fmt.Errorf(
 			"illegal flag value --%s %s; legal values: %v",
 			flagReorderOutputName, theFlags.reorderOutput,
-			[]string{legacy.String(), none.String()})
+			[]string{legacy.String(), none.String(), unspecified.String()})
 	}
 }
 
-func getFlagReorderOutput() reorderOutput {
+func getFlagReorderOutput() krusty.ReorderOption {
 	switch theFlags.reorderOutput {
 	case none.String():
-		return none
+		return krusty.ReorderOptionNone
 	case legacy.String():
-		return legacy
+		return krusty.ReorderOptionLegacy
 	default:
-		return unspecified
+		return krusty.ReorderOptionUnspecified
 	}
 }