diff --git a/cmd/commands_test.go b/cmd/commands_test.go
index 266fb2c6..271eb52c 100644
--- a/cmd/commands_test.go
+++ b/cmd/commands_test.go
@@ -1872,14 +1872,16 @@ c:
 	test.AssertResult(t, os.FileMode(int(0666)), info.Mode())
 }
 
-func TestMergeAllowEmptyCmd(t *testing.T) {
+func TestMergeAllowEmptyTargetCmd(t *testing.T) {
 	cmd := getRootCommand()
-	result := test.RunCmd(cmd, "merge --allow-empty ../examples/data1.yaml ../examples/empty.yaml")
+	result := test.RunCmd(cmd, "merge ../examples/empty.yaml ../examples/data1.yaml")
 	if result.Error != nil {
 		t.Error(result.Error)
 	}
 	expectedOutput := `a: simple # just the best
-b: [1, 2]
+b:
+- 1
+- 2
 c:
   test: 1
 `
diff --git a/cmd/constant.go b/cmd/constant.go
index 4c1c340e..7d5d590e 100644
--- a/cmd/constant.go
+++ b/cmd/constant.go
@@ -15,7 +15,6 @@ var defaultValue = ""
 var indent = 2
 var overwriteFlag = false
 var autoCreateFlag = true
-var allowEmptyFlag = false
 var appendFlag = false
 var verbose = false
 var version = false
diff --git a/cmd/merge.go b/cmd/merge.go
index 0d9905ae..645eb30d 100644
--- a/cmd/merge.go
+++ b/cmd/merge.go
@@ -1,8 +1,6 @@
 package cmd
 
 import (
-	"strings"
-
 	"github.com/mikefarah/yq/v3/pkg/yqlib"
 	errors "github.com/pkg/errors"
 	"github.com/spf13/cobra"
@@ -34,7 +32,6 @@ If append flag is set then existing arrays will be merged with the arrays from e
 	cmdMerge.PersistentFlags().BoolVarP(&overwriteFlag, "overwrite", "x", false, "update the yaml file by overwriting existing values")
 	cmdMerge.PersistentFlags().BoolVarP(&autoCreateFlag, "autocreate", "c", true, "automatically create any missing entries")
 	cmdMerge.PersistentFlags().BoolVarP(&appendFlag, "append", "a", false, "update the yaml file by appending array values")
-	cmdMerge.PersistentFlags().BoolVarP(&allowEmptyFlag, "allow-empty", "e", false, "allow empty yaml files")
 	cmdMerge.PersistentFlags().StringVarP(&docIndex, "doc", "d", "0", "process document index number (0 based, * for all documents)")
 	return cmdMerge
 }
@@ -52,7 +49,7 @@ func mergeProperties(cmd *cobra.Command, args []string) error {
 
 		for _, fileToMerge := range filesToMerge {
 			matchingNodes, errorProcessingFile := readYamlFile(fileToMerge, "**", false, 0)
-			if errorProcessingFile != nil && (!allowEmptyFlag || !strings.HasPrefix(errorProcessingFile.Error(), "Could not process document index")) {
+			if errorProcessingFile != nil {
 				return errorProcessingFile
 			}
 			for _, matchingNode := range matchingNodes {