diff --git a/pkg/config/config.go b/pkg/config/config.go
index 446fff5ba31..870a838809e 100644
--- a/pkg/config/config.go
+++ b/pkg/config/config.go
@@ -452,11 +452,17 @@ func (c *Config) UpdateFromFile(path string) error {
 	t := new(tomlConfig)
 	t.fromConfig(c)
 
-	_, err = toml.Decode(string(data), t)
+	metadata, err := toml.Decode(string(data), t)
 	if err != nil {
 		return fmt.Errorf("unable to decode configuration %v: %v", path, err)
 	}
 
+	runtimesKey := []string{"crio", "runtime", "default_runtime"}
+	if metadata.IsDefined(runtimesKey...) &&
+		t.Crio.Runtime.RuntimeConfig.DefaultRuntime != defaultRuntime {
+		delete(c.Runtimes, defaultRuntime)
+	}
+
 	t.toConfig(c)
 	c.singleConfigPath = path
 	return nil
diff --git a/pkg/config/template.go b/pkg/config/template.go
index c42f42f64d1..34abe6aace8 100644
--- a/pkg/config/template.go
+++ b/pkg/config/template.go
@@ -110,7 +110,8 @@ grpc_max_recv_msg_size = {{ .GRPCMaxRecvMsgSize }}
 {{ range $ulimit := .DefaultUlimits }}{{ printf "#\t%q,\n" $ulimit }}{{ end }}#]
 
 # default_runtime is the _name_ of the OCI runtime to be used as the default.
-# The name is matched against the runtimes map below.
+# The name is matched against the runtimes map below. If this value is changed,
+# the corresponding existing entry from the runtimes map below will be ignored.
 default_runtime = "{{ .DefaultRuntime }}"
 
 # If true, the runtime will not use pivot_root, but instead use MS_MOVE.