diff --git a/cmd/clusterctl/clusterdeployer/clusterdeployer.go b/cmd/clusterctl/clusterdeployer/clusterdeployer.go
index 66509685f872..72faf9d33a93 100644
--- a/cmd/clusterctl/clusterdeployer/clusterdeployer.go
+++ b/cmd/clusterctl/clusterdeployer/clusterdeployer.go
@@ -102,18 +102,12 @@ func (d *ClusterDeployer) Create(cluster *clusterv1.Cluster, machines []*cluster
 		return fmt.Errorf("unable to create cluster %q in bootstrap cluster: %v", cluster.Name, err)
 	}
 
-	// Create initial controlplane instance
 	if cluster.Namespace == "" {
 		cluster.Namespace = bootstrapClient.GetContextNamespace()
 	}
 
-	err = bootstrapClient.EnsureNamespace(cluster.Namespace)
-	if err != nil {
-		return fmt.Errorf("unable to ensure namespace %q in bootstrap cluster: %v", cluster.Namespace, err)
-	}
-
 	glog.Infof("Creating master %v in namespace %q", master.Name, cluster.Namespace)
-	if err := bootstrapClient.CreateMachineObjects([]*clusterv1.Machine{master}, cluster.Namespace); err != nil {
+	if err := phases.ApplyMachines(bootstrapClient, cluster.Namespace, []*clusterv1.Machine{master}); err != nil {
 		return fmt.Errorf("unable to create master machine: %v", err)
 	}
 
@@ -160,7 +154,7 @@ func (d *ClusterDeployer) Create(cluster *clusterv1.Cluster, machines []*cluster
 	}
 
 	glog.Info("Creating node machines in target cluster.")
-	if err := targetClient.CreateMachineObjects(nodes, cluster.Namespace); err != nil {
+	if err := phases.ApplyMachines(bootstrapClient, cluster.Namespace, nodes); err != nil {
 		return fmt.Errorf("unable to create node machines: %v", err)
 	}
 
diff --git a/cmd/clusterctl/cmd/alpha_phase_apply_machines.go b/cmd/clusterctl/cmd/alpha_phase_apply_machines.go
new file mode 100644
index 000000000000..b7bb0e224cd6
--- /dev/null
+++ b/cmd/clusterctl/cmd/alpha_phase_apply_machines.go
@@ -0,0 +1,89 @@
+/*
+Copyright 2018 The Kubernetes Authors.
+
+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 cmd
+
+import (
+	"fmt"
+	"io/ioutil"
+
+	"github.com/golang/glog"
+	"github.com/spf13/cobra"
+	"sigs.k8s.io/cluster-api/cmd/clusterctl/clusterdeployer/clusterclient"
+	"sigs.k8s.io/cluster-api/cmd/clusterctl/phases"
+	"sigs.k8s.io/cluster-api/pkg/util"
+)
+
+type AlphaPhaseApplyMachinesOptions struct {
+	Kubeconfig string
+	Machines   string
+	Namespace  string
+}
+
+var pamo = &AlphaPhaseApplyMachinesOptions{}
+
+var alphaPhaseApplyMachinesCmd = &cobra.Command{
+	Use:   "apply-machines",
+	Short: "Apply Machines",
+	Long:  `Apply Machines`,
+	Run: func(cmd *cobra.Command, args []string) {
+		if pamo.Machines == "" {
+			exitWithHelp(cmd, "Please provide yaml file for machines definition.")
+		}
+
+		if pamo.Kubeconfig == "" {
+			exitWithHelp(cmd, "Please provide a kubeconfig file.")
+		}
+
+		if err := RunAlphaPhaseApplyMachines(pamo); err != nil {
+			glog.Exit(err)
+		}
+	},
+}
+
+func RunAlphaPhaseApplyMachines(pamo *AlphaPhaseApplyMachinesOptions) error {
+	kubeconfig, err := ioutil.ReadFile(pamo.Kubeconfig)
+	if err != nil {
+		return err
+	}
+
+	machines, err := util.ParseMachinesYaml(pamo.Machines)
+	if err != nil {
+		return err
+	}
+
+	clientFactory := clusterclient.NewFactory()
+	client, err := clientFactory.NewClientFromKubeconfig(string(kubeconfig))
+	if err != nil {
+		return fmt.Errorf("unable to create cluster client: %v", err)
+	}
+
+	if err := phases.ApplyMachines(client, pamo.Namespace, machines); err != nil {
+		return fmt.Errorf("unable to apply machines: %v", err)
+	}
+
+	return nil
+}
+
+func init() {
+	// Required flags
+	alphaPhaseApplyMachinesCmd.Flags().StringVarP(&pamo.Kubeconfig, "kubeconfig", "", "", "Path for the kubeconfig file to use")
+	alphaPhaseApplyMachinesCmd.Flags().StringVarP(&pamo.Machines, "machines", "m", "", "A yaml file containing machine object definitions")
+
+	// Optional flags
+	alphaPhaseApplyMachinesCmd.Flags().StringVarP(&pamo.Namespace, "namespace", "n", "", "Namespace")
+	alphaPhasesCmd.AddCommand(alphaPhaseApplyMachinesCmd)
+}
diff --git a/cmd/clusterctl/phases/applymachines.go b/cmd/clusterctl/phases/applymachines.go
new file mode 100644
index 000000000000..b14e362af3a0
--- /dev/null
+++ b/cmd/clusterctl/phases/applymachines.go
@@ -0,0 +1,43 @@
+/*
+Copyright 2018 The Kubernetes Authors.
+
+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 phases
+
+import (
+	"fmt"
+
+	"github.com/golang/glog"
+	"sigs.k8s.io/cluster-api/cmd/clusterctl/clusterdeployer/clusterclient"
+	clusterv1 "sigs.k8s.io/cluster-api/pkg/apis/cluster/v1alpha1"
+)
+
+func ApplyMachines(client clusterclient.Client, namespace string, machines []*clusterv1.Machine) error {
+	if namespace == "" {
+		namespace = client.GetContextNamespace()
+	}
+
+	err := client.EnsureNamespace(namespace)
+	if err != nil {
+		return fmt.Errorf("unable to ensure namespace %q: %v", namespace, err)
+	}
+
+	glog.Infof("Creating machines in namespace %q", namespace)
+	if err := client.CreateMachineObjects(machines, namespace); err != nil {
+		return err
+	}
+
+	return nil
+}