diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 864fe7cc3..8baa3f855 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -427,8 +427,9 @@ jobs:
           BDIR="$(mktemp -d -p $PWD)"
           mkdir -p ${BDIR}/{root,state}
           cat > ${BDIR}/config.toml <<EOF
-            [plugins.cri.containerd.default_runtime]
-              runtime_type = "${TEST_RUNTIME}"
+            version = 2
+            [plugins."io.containerd.grpc.v1.cri".containerd.runtimes.runc]
+            runtime_type = "${TEST_RUNTIME}"
           EOF
           sudo ls /etc/cni/net.d
           sudo PATH=$PATH BDIR=$BDIR /usr/local/bin/containerd -a ${BDIR}/c.sock --config ${BDIR}/config.toml --root ${BDIR}/root --state ${BDIR}/state --log-level debug &> ${BDIR}/containerd-cri.log &
diff --git a/RELEASES.md b/RELEASES.md
index e58a00ba8..133e4d1bd 100644
--- a/RELEASES.md
+++ b/RELEASES.md
@@ -294,7 +294,8 @@ The daemon's configuration file, commonly located in `/etc/containerd/config.tom
 is versioned and backwards compatible.  The `version` field in the config
 file specifies the config's version.  If no version number is specified inside
 the config file then it is assumed to be a version 1 config and parsed as such.
-Use `version = 2` to enable version 2 config.
+Please use `version = 2` to enable version 2 config as version 1 has been
+deprecated.
 
 ### Not Covered
 
@@ -324,3 +325,4 @@ The deprecated features are shown in the following table:
 |----------------------------------------------------------------------|---------------------|----------------------------|
 | Runtime V1 API and implementation (`io.containerd.runtime.v1.linux`) | containerd v1.4     | containerd v2.0            |
 | Runc V1 implementation of Runtime V2 (`io.containerd.runc.v1`)       | containerd v1.4     | containerd v2.0            |
+| config.toml `version = 1`                                            | containerd v1.5     | containerd v2.0            |
diff --git a/cmd/containerd/command/config.go b/cmd/containerd/command/config.go
index 7282f476c..8ba6deef0 100644
--- a/cmd/containerd/command/config.go
+++ b/cmd/containerd/command/config.go
@@ -120,7 +120,7 @@ var configCommand = cli.Command{
 
 func platformAgnosticDefaultConfig() *srvconfig.Config {
 	return &srvconfig.Config{
-		Version: 1,
+		Version: 2,
 		Root:    defaults.DefaultRootDir,
 		State:   defaults.DefaultStateDir,
 		GRPC: srvconfig.GRPCConfig{
diff --git a/integration/client/client_test.go b/integration/client/client_test.go
index 109ec3c7a..022669ae1 100644
--- a/integration/client/client_test.go
+++ b/integration/client/client_test.go
@@ -503,12 +503,12 @@ func createShimDebugConfig() string {
 		os.Exit(1)
 	}
 	defer f.Close()
-	if _, err := f.WriteString("version = 1\n"); err != nil {
+	if _, err := f.WriteString("version = 2\n"); err != nil {
 		fmt.Fprintf(os.Stderr, "Failed to write to config file %s: %s\n", f.Name(), err)
 		os.Exit(1)
 	}
 
-	if _, err := f.WriteString("[plugins.linux]\n\tshim_debug = true\n"); err != nil {
+	if _, err := f.WriteString("[plugins.\"io.containerd.runtime.v1.linux\"]\n\tshim_debug = true\n"); err != nil {
 		fmt.Fprintf(os.Stderr, "Failed to write to config file %s: %s\n", f.Name(), err)
 		os.Exit(1)
 	}
diff --git a/integration/client/daemon_config_linux_test.go b/integration/client/daemon_config_linux_test.go
index 18d425e50..d62e93877 100644
--- a/integration/client/daemon_config_linux_test.go
+++ b/integration/client/daemon_config_linux_test.go
@@ -129,9 +129,9 @@ func TestDaemonRuntimeRoot(t *testing.T) {
 		}
 	}()
 	configTOML := `
-version = 1
+version = 2
 [plugins]
- [plugins.cri]
+ [plugins."io.containerd.grpc.v1.cri"]
    stream_server_port = "0"
 `
 
@@ -227,7 +227,7 @@ func TestDaemonCustomCgroup(t *testing.T) {
 
 	customCgroup := fmt.Sprintf("%d", time.Now().Nanosecond())
 	configTOML := `
-version = 1
+version = 2
 [cgroup]
   path = "` + customCgroup + `"`
 
diff --git a/script/test/utils.sh b/script/test/utils.sh
index e2819d1f1..6093bf8be 100755
--- a/script/test/utils.sh
+++ b/script/test/utils.sh
@@ -30,14 +30,15 @@ if [ -z "${CONTAINERD_CONFIG_FILE}" ]; then
   truncate --size 0 "${config_file}"
   if command -v sestatus >/dev/null 2>&1; then
     cat >>${config_file} <<EOF
-[plugins.cri]
+version=2
+[plugins."io.containerd.grpc.v1.cri"]
   enable_selinux = true
 EOF
   fi
   if [ -n "${CONTAINERD_RUNTIME}" ]; then
     cat >>${config_file} <<EOF
-[plugins.cri.containerd.default_runtime]
-  runtime_type="${CONTAINERD_RUNTIME}"
+[plugins."io.containerd.grpc.v1.cri".containerd.runtimes.runc]
+runtime_type = "${CONTAINERD_RUNTIME}"
 EOF
   fi
   CONTAINERD_CONFIG_FILE="${config_file}"
diff --git a/services/server/config/config.go b/services/server/config/config.go
index f82cfb310..ff0639167 100644
--- a/services/server/config/config.go
+++ b/services/server/config/config.go
@@ -23,6 +23,7 @@ import (
 	"github.com/imdario/mergo"
 	"github.com/pelletier/go-toml"
 	"github.com/pkg/errors"
+	"github.com/sirupsen/logrus"
 
 	"github.com/containerd/containerd/errdefs"
 	"github.com/containerd/containerd/plugin"
@@ -94,8 +95,9 @@ func (c *Config) GetVersion() int {
 
 // ValidateV2 validates the config for a v2 file
 func (c *Config) ValidateV2() error {
-	if c.GetVersion() != 2 {
-		return nil
+	version := c.GetVersion()
+	if version < 2 {
+		logrus.Warnf("deprecated version : `%d`, please switch to version `2`", version)
 	}
 	for _, p := range c.DisabledPlugins {
 		if len(strings.Split(p, ".")) < 4 {
@@ -258,7 +260,11 @@ func LoadConfig(path string, out *Config) error {
 		out.Imports = append(out.Imports, path)
 	}
 
-	return out.ValidateV2()
+	err := out.ValidateV2()
+	if err != nil {
+		return errors.Wrapf(err, "failed to load TOML from %s", path)
+	}
+	return nil
 }
 
 // loadConfigFile decodes a TOML file at the given path
diff --git a/services/server/config/config_test.go b/services/server/config/config_test.go
index 47a12f17b..3bcee7eff 100644
--- a/services/server/config/config_test.go
+++ b/services/server/config/config_test.go
@@ -185,8 +185,8 @@ imports = ["data1.toml", "data2.toml"]
 
 func TestDecodePlugin(t *testing.T) {
 	data := `
-version = 1
-[plugins.linux]
+version = 2
+[plugins."io.containerd.runtime.v1.linux"]
   shim_debug = true
 `
 
@@ -203,7 +203,7 @@ version = 1
 	assert.NilError(t, err)
 
 	pluginConfig := map[string]interface{}{}
-	_, err = out.Decode(&plugin.Registration{ID: "linux", Config: &pluginConfig})
+	_, err = out.Decode(&plugin.Registration{Type: "io.containerd.runtime.v1", ID: "linux", Config: &pluginConfig})
 	assert.NilError(t, err)
 	assert.Equal(t, true, pluginConfig["shim_debug"])
 }