diff --git a/cmd/config/configMigrate.go b/cmd/config/configMigrate.go
index 4b79615f..d0e80d0c 100644
--- a/cmd/config/configMigrate.go
+++ b/cmd/config/configMigrate.go
@@ -100,7 +100,7 @@ func NewCmdConfigMigrate() *cobra.Command {
 					l.Log().Fatalln(err)
 				}
 			} else {
-				if err := os.WriteFile(output, yamlout, os.ModeAppend); err != nil {
+				if err := os.WriteFile(output, yamlout, os.ModePerm); err != nil {
 					l.Log().Fatalln(err)
 				}
 			}
diff --git a/pkg/config/v1alpha3/migrations.go b/pkg/config/v1alpha3/migrations.go
index 0faeff1b..5b20c9bb 100644
--- a/pkg/config/v1alpha3/migrations.go
+++ b/pkg/config/v1alpha3/migrations.go
@@ -25,11 +25,13 @@ package v1alpha3
 import (
 	"encoding/json"
 	"fmt"
+	"strings"
 
 	configtypes "github.com/rancher/k3d/v5/pkg/config/types"
 	"github.com/rancher/k3d/v5/pkg/config/v1alpha2"
 	l "github.com/rancher/k3d/v5/pkg/logger"
 	k3d "github.com/rancher/k3d/v5/pkg/types"
+	"github.com/rancher/k3d/v5/pkg/util"
 )
 
 var Migrations = map[string]func(configtypes.Config) (configtypes.Config, error){
@@ -39,11 +41,23 @@ var Migrations = map[string]func(configtypes.Config) (configtypes.Config, error)
 func MigrateV1Alpha2(input configtypes.Config) (configtypes.Config, error) {
 	l.Log().Debugln("Migrating v1alpha2 to v1alpha3")
 
+	// nodefilters changed from `@group[index]` to `@group:index`
+	nodeFilterReplacer := strings.NewReplacer(
+		"[", ":", // replace opening bracket
+		"]", "", // drop closing bracket
+	)
+
+	/*
+	 * We're migrating matching fields between versions by marshalling to JSON and back
+	 */
 	injson, err := json.Marshal(input)
 	if err != nil {
 		return nil, err
 	}
 
+	/*
+	 * Migrate config of `kind: Simple`
+	 */
 	if input.GetKind() == "Simple" {
 		cfgIntermediate := SimpleConfigIntermediateV1alpha2{}
 
@@ -60,15 +74,20 @@ func MigrateV1Alpha2(input configtypes.Config) (configtypes.Config, error) {
 			return nil, err
 		}
 
+		// simple nodefilter changes
 		cfg.Options.Runtime.Labels = []LabelWithNodeFilters{}
 
 		for _, label := range input.(v1alpha2.SimpleConfig).Labels {
 			cfg.Options.Runtime.Labels = append(cfg.Options.Runtime.Labels, LabelWithNodeFilters{
 				Label:       label.Label,
-				NodeFilters: label.NodeFilters,
+				NodeFilters: util.ReplaceInAllElements(nodeFilterReplacer, label.NodeFilters),
 			})
 		}
 
+		/*
+		 * structural changes (e.g. added nodefilter support)
+		 */
+
 		cfg.Options.K3sOptions.ExtraArgs = []K3sArgWithNodeFilters{}
 
 		for _, arg := range input.(v1alpha2.SimpleConfig).Options.K3sOptions.ExtraServerArgs {
@@ -97,6 +116,25 @@ func MigrateV1Alpha2(input configtypes.Config) (configtypes.Config, error) {
 			}
 		}
 
+		/*
+		 * Matching fields with only syntactical changes (e.g. nodefilter syntax changed)
+		 */
+		for _, env := range cfg.Env {
+			env.NodeFilters = util.ReplaceInAllElements(nodeFilterReplacer, env.NodeFilters)
+		}
+
+		for _, vol := range cfg.Volumes {
+			vol.NodeFilters = util.ReplaceInAllElements(nodeFilterReplacer, vol.NodeFilters)
+		}
+
+		for _, p := range cfg.Ports {
+			p.NodeFilters = util.ReplaceInAllElements(nodeFilterReplacer, p.NodeFilters)
+		}
+
+		/*
+		 * Finalizing
+		 */
+
 		cfg.APIVersion = ApiVersion
 
 		l.Log().Debugf("Migrated config: %+v", cfg)
diff --git a/pkg/util/util.go b/pkg/util/util.go
index 0fa9cda2..9d760172 100644
--- a/pkg/util/util.go
+++ b/pkg/util/util.go
@@ -22,7 +22,16 @@ THE SOFTWARE.
 
 package util
 
+import "strings"
+
 func RemoveElementFromStringSlice(slice []string, index int) []string {
 	slice[index] = slice[len(slice)-1]
 	return slice[:len(slice)-1]
 }
+
+func ReplaceInAllElements(replacer *strings.Replacer, arr []string) []string {
+	for i, elem := range arr {
+		arr[i] = replacer.Replace(elem)
+	}
+	return arr
+}
diff --git a/tests/assets/config_test_simple_migration_v1alpha2.yaml b/tests/assets/config_test_simple_migration_v1alpha2.yaml
index 49fb1bfe..e58d896c 100755
--- a/tests/assets/config_test_simple_migration_v1alpha2.yaml
+++ b/tests/assets/config_test_simple_migration_v1alpha2.yaml
@@ -25,7 +25,7 @@ env:
 labels:
   - label: foo=bar
     nodeFilters:
-      - server:0
+      - server[0]
       - loadbalancer
 registries:
   create: true