diff --git a/cmd/containerd/server/config/config.go b/cmd/containerd/server/config/config.go
index 3962cd9f4..ac0a6e8a5 100644
--- a/cmd/containerd/server/config/config.go
+++ b/cmd/containerd/server/config/config.go
@@ -30,6 +30,7 @@ import (
 	"io"
 	"os"
 	"path/filepath"
+	"reflect"
 	"strings"
 
 	"dario.cat/mergo"
@@ -310,12 +311,6 @@ func LoadConfig(ctx context.Context, path string, out *Config) error {
 		pending = append(pending, imports...)
 	}
 
-	// Fix up the list of config files loaded
-	out.Imports = []string{}
-	for path := range loaded {
-		out.Imports = append(out.Imports, path)
-	}
-
 	err := out.ValidateVersion()
 	if err != nil {
 		return fmt.Errorf("failed to load TOML from %s: %w", path, err)
@@ -408,9 +403,11 @@ func resolveImports(parent string, imports []string) ([]string, error) {
 // 0            1           1
 // []{"1"}      []{"2"}     []{"1","2"}
 // []{"1"}      []{}        []{"1"}
+// []{"1", "2"} []{"1"}     []{"1","2"}
+// []{}         []{"2"}     []{"2"}
 // Maps merged by keys, but values are replaced entirely.
 func mergeConfig(to, from *Config) error {
-	err := mergo.Merge(to, from, mergo.WithOverride, mergo.WithAppendSlice)
+	err := mergo.Merge(to, from, mergo.WithOverride, mergo.WithTransformers(sliceTransformer{}))
 	if err != nil {
 		return err
 	}
@@ -435,6 +432,43 @@ func mergeConfig(to, from *Config) error {
 	return nil
 }
 
+type sliceTransformer struct{}
+
+func (sliceTransformer) Transformer(t reflect.Type) func(dst, src reflect.Value) error {
+	if t.Kind() != reflect.Slice {
+		return nil
+	}
+	return func(dst, src reflect.Value) error {
+		if !dst.CanSet() {
+			return nil
+		}
+		if src.Type() != dst.Type() {
+			return fmt.Errorf("cannot append two slice with different type (%s, %s)", src.Type(), dst.Type())
+		}
+		for i := 0; i < src.Len(); i++ {
+			found := false
+			for j := 0; j < dst.Len(); j++ {
+				srcv := src.Index(i)
+				dstv := dst.Index(j)
+				if !srcv.CanInterface() || !dstv.CanInterface() {
+					if srcv.Equal(dstv) {
+						found = true
+						break
+					}
+				} else if reflect.DeepEqual(srcv.Interface(), dstv.Interface()) {
+					found = true
+					break
+				}
+			}
+			if !found {
+				dst.Set(reflect.Append(dst, src.Index(i)))
+			}
+		}
+
+		return nil
+	}
+}
+
 // V2DisabledFilter matches based on URI
 func V2DisabledFilter(list []string) plugin.DisableFilter {
 	set := make(map[string]struct{}, len(list))
diff --git a/cmd/containerd/server/config/config_test.go b/cmd/containerd/server/config/config_test.go
index 39d3a6616..817e82028 100644
--- a/cmd/containerd/server/config/config_test.go
+++ b/cmd/containerd/server/config/config_test.go
@@ -50,6 +50,7 @@ func TestMergeConfigs(t *testing.T) {
 		Version:          2,
 		Root:             "new_root",
 		RequiredPlugins:  []string{"io.containerd.new_plugin1.v1", "io.containerd.new_plugin2.v1"},
+		DisabledPlugins:  []string{"io.containerd.old_plugin.v1"},
 		OOMScore:         2,
 		Timeouts:         map[string]string{"b": "2"},
 		StreamProcessors: map[string]StreamProcessor{"1": {Path: "3"}},
@@ -191,8 +192,8 @@ imports = ["data1.toml", "data2.toml"]
 
 	sort.Strings(out.Imports)
 	assert.Equal(t, []string{
-		filepath.Join(tempDir, "data1.toml"),
-		filepath.Join(tempDir, "data2.toml"),
+		"data1.toml",
+		"data2.toml",
 	}, out.Imports)
 }