diff --git a/cmd/config/config.go b/cmd/config/config.go
index b342acdfe..2ff51ca1f 100644
--- a/cmd/config/config.go
+++ b/cmd/config/config.go
@@ -448,6 +448,11 @@ func (c Config) Merge() Config {
 					ckvs.Set(kv.Key, kv.Value)
 				}
 			}
+			if _, ok := cp[subSys]; !ok {
+				// A config subsystem was removed or server was downgraded.
+				Logger.Info("config: ignoring unknown subsystem config %q\n", subSys)
+				continue
+			}
 			cp[subSys][tgt] = ckvs
 		}
 	}
diff --git a/cmd/config/logger.go b/cmd/config/logger.go
new file mode 100644
index 000000000..096045c8d
--- /dev/null
+++ b/cmd/config/logger.go
@@ -0,0 +1,27 @@
+/*
+ * MinIO Cloud Storage, (C) 2020 MinIO, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package config
+
+import "context"
+
+// Logger contains injected logger methods.
+var Logger = struct {
+	Info  func(msg string, data ...interface{})
+	LogIf func(ctx context.Context, err error, errKind ...interface{})
+}{
+	// Initialized via injection.
+}
diff --git a/cmd/logger/config.go b/cmd/logger/config.go
index dc520f832..2cc6e71f3 100644
--- a/cmd/logger/config.go
+++ b/cmd/logger/config.go
@@ -56,6 +56,12 @@ const (
 	EnvAuditWebhookAuthToken = "MINIO_AUDIT_WEBHOOK_AUTH_TOKEN"
 )
 
+// Inject into config package.
+func init() {
+	config.Logger.Info = Info
+	config.Logger.LogIf = LogIf
+}
+
 // Default KVS for loggerHTTP and loggerAuditHTTP
 var (
 	DefaultKVS = config.KVS{