diff --git a/config/config.go b/config/config.go
index 93494265d05..bc8ea371f17 100644
--- a/config/config.go
+++ b/config/config.go
@@ -83,7 +83,7 @@ func Path(configroot, extension string) (string, error) {
 //   - If the user-provided configuration file path is only a file name, use the
 //     configuration root directory, otherwise use only the user-provided path
 //     and ignore the configuration root.
-func Filename(configroot string, userConfigFile string) (string, error) {
+func Filename(configroot, userConfigFile string) (string, error) {
 	if userConfigFile == "" {
 		return Path(configroot, DefaultConfigFile)
 	}
diff --git a/config/types.go b/config/types.go
index a781f023af9..2171a53f5bd 100644
--- a/config/types.go
+++ b/config/types.go
@@ -415,9 +415,9 @@ func (p OptionalString) String() string {
 var _ json.Unmarshaler = (*OptionalInteger)(nil)
 var _ json.Marshaler = (*OptionalInteger)(nil)
 
-type swarmLimits struct{}
+type swarmLimits doNotUse
 
-var _ json.Unmarshaler = swarmLimits{}
+var _ json.Unmarshaler = swarmLimits(false)
 
 func (swarmLimits) UnmarshalJSON(b []byte) error {
 	d := json.NewDecoder(bytes.NewReader(b))
@@ -439,9 +439,9 @@ func (swarmLimits) UnmarshalJSON(b []byte) error {
 	}
 }
 
-type experimentalAcceleratedDHTClient struct{}
+type experimentalAcceleratedDHTClient doNotUse
 
-var _ json.Unmarshaler = experimentalAcceleratedDHTClient{}
+var _ json.Unmarshaler = experimentalAcceleratedDHTClient(false)
 
 func (experimentalAcceleratedDHTClient) UnmarshalJSON(b []byte) error {
 	d := json.NewDecoder(bytes.NewReader(b))
@@ -462,3 +462,8 @@ func (experimentalAcceleratedDHTClient) UnmarshalJSON(b []byte) error {
 		}
 	}
 }
+
+// doNotUse is a type you must not use, it should be struct{} but encoding/json
+// does not support omitempty on structs and I can't be bothered to write custom
+// marshalers on all structs that have a doNotUse field.
+type doNotUse bool
diff --git a/plugin/loader/loader.go b/plugin/loader/loader.go
index f891bb570f4..84ebdc0fc40 100644
--- a/plugin/loader/loader.go
+++ b/plugin/loader/loader.go
@@ -1,6 +1,7 @@
 package loader
 
 import (
+	"encoding/json"
 	"fmt"
 	"io"
 	"os"
@@ -9,7 +10,6 @@ import (
 	"strings"
 
 	config "github.com/ipfs/kubo/config"
-	cserialize "github.com/ipfs/kubo/config/serialize"
 	"github.com/ipld/go-ipld-prime/multicodec"
 
 	"github.com/ipfs/kubo/core"
@@ -97,11 +97,10 @@ type PluginLoader struct {
 func NewPluginLoader(repo string) (*PluginLoader, error) {
 	loader := &PluginLoader{plugins: make([]plugin.Plugin, 0, len(preloadPlugins)), repo: repo}
 	if repo != "" {
-		cfg, err := cserialize.Load(filepath.Join(repo, config.DefaultConfigFile))
-		switch err {
-		case cserialize.ErrNotInitialized:
-		case nil:
-			loader.config = cfg.Plugins
+		switch plugins, err := readPluginsConfig(repo, config.DefaultConfigFile); {
+		case err == nil:
+			loader.config = plugins
+		case os.IsNotExist(err):
 		default:
 			return nil, err
 		}
@@ -119,6 +118,33 @@ func NewPluginLoader(repo string) (*PluginLoader, error) {
 	return loader, nil
 }
 
+// readPluginsConfig reads the Plugins section of the IPFS config, avoiding
+// reading anything other than the Plugin section. That way, we're free to
+// make arbitrary changes to all _other_ sections in migrations.
+func readPluginsConfig(repoRoot string, userConfigFile string) (config.Plugins, error) {
+	var cfg struct {
+		Plugins config.Plugins
+	}
+
+	cfgPath, err := config.Filename(repoRoot, userConfigFile)
+	if err != nil {
+		return config.Plugins{}, err
+	}
+
+	cfgFile, err := os.Open(cfgPath)
+	if err != nil {
+		return config.Plugins{}, err
+	}
+	defer cfgFile.Close()
+
+	err = json.NewDecoder(cfgFile).Decode(&cfg)
+	if err != nil {
+		return config.Plugins{}, err
+	}
+
+	return cfg.Plugins, nil
+}
+
 func (loader *PluginLoader) assertState(state loaderState) error {
 	if loader.state != state {
 		return fmt.Errorf("loader state must be %s, was %s", state, loader.state)