diff --git a/kyaml/kio/kio.go b/kyaml/kio/kio.go
index 32bdebb32..91efde1d9 100644
--- a/kyaml/kio/kio.go
+++ b/kyaml/kio/kio.go
@@ -99,10 +99,6 @@ func (p Pipeline) ExecuteWithCallback(callback PipelineExecuteCallbackFunc) erro
 		}
 		result = append(result, nodes...)
 	}
-	if len(result) == 0 {
-		// no inputs to operate on
-		return nil
-	}
 
 	// apply operations
 	var err error
@@ -112,6 +108,9 @@ func (p Pipeline) ExecuteWithCallback(callback PipelineExecuteCallbackFunc) erro
 			callback(op)
 		}
 		result, err = op.Filter(result)
+		// TODO (issue 2872): This len(result) == 0 should be removed and empty result list should be
+		// handled by outputs. However currently some writer like LocalPackageReadWriter
+		// will clear the output directory and which will cause unpredictable results
 		if len(result) == 0 || err != nil {
 			return errors.Wrap(err)
 		}
diff --git a/kyaml/kio/kio_test.go b/kyaml/kio/kio_test.go
index d51301d9b..9a3a9ea27 100644
--- a/kyaml/kio/kio_test.go
+++ b/kyaml/kio/kio_test.go
@@ -4,7 +4,9 @@
 package kio_test
 
 import (
+	"bytes"
 	"reflect"
+	"strings"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
@@ -75,3 +77,75 @@ func TestPipelineWithCallback(t *testing.T) {
 		)
 	}
 }
+
+func TestEmptyInput(t *testing.T) {
+	actual := &bytes.Buffer{}
+	output := ByteWriter{
+		Sort:               true,
+		WrappingKind:       ResourceListKind,
+		WrappingAPIVersion: ResourceListAPIVersion,
+	}
+	output.Writer = actual
+
+	p := Pipeline{
+		Outputs: []Writer{output},
+	}
+
+	err := p.Execute()
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	expected := `
+apiVersion: config.kubernetes.io/v1alpha1
+kind: ResourceList
+items: []
+`
+
+	if !assert.Equal(t,
+		strings.TrimSpace(expected), strings.TrimSpace(actual.String())) {
+		t.FailNow()
+	}
+}
+
+func TestEmptyInputWithFilter(t *testing.T) {
+	actual := &bytes.Buffer{}
+	output := ByteWriter{
+		Sort:               true,
+		WrappingKind:       ResourceListKind,
+		WrappingAPIVersion: ResourceListAPIVersion,
+	}
+	output.Writer = actual
+
+	filters := []Filter{
+		FilterFunc(func(nodes []*yaml.RNode) ([]*yaml.RNode, error) {
+			nodes = append(nodes, yaml.NewMapRNode(&map[string]string{
+				"foo": "bar",
+			}))
+			return nodes, nil
+		}),
+		FilterFunc(func(nodes []*yaml.RNode) ([]*yaml.RNode, error) { return nodes, nil }),
+	}
+
+	p := Pipeline{
+		Outputs: []Writer{output},
+		Filters: filters,
+	}
+
+	err := p.Execute()
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	expected := `
+apiVersion: config.kubernetes.io/v1alpha1
+kind: ResourceList
+items:
+- foo: bar
+`
+
+	if !assert.Equal(t,
+		strings.TrimSpace(expected), strings.TrimSpace(actual.String())) {
+		t.FailNow()
+	}
+}