diff --git a/Dockerfile b/Dockerfile
index eb064c1c..d9ddf6ca 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -9,8 +9,10 @@ COPY static/ /static/
 
 RUN \
  apk --no-cache add curl ca-certificates git go musl-dev && \
- curl -sSL -o /usr/local/bin/kubectl https://storage.googleapis.com/kubernetes-release/release/v1.9.3/bin/linux/amd64/kubectl && \
+ curl -sSL -o /usr/local/bin/kubectl https://storage.googleapis.com/kubernetes-release/release/v1.10.4/bin/linux/amd64/kubectl && \
+ curl -sSL -o /usr/local/bin/kustomize https://github.com/kubernetes-sigs/kustomize/releases/download/v1.0.3/kustomize_1.0.3_linux_amd64 && \
  chmod +x /usr/local/bin/kubectl && \
+ chmod +x /usr/local/bin/kustomize && \
  go get -t ./... && \
  go test ./... && \
  CGO_ENABLED=0 go build -ldflags '-s -extldflags "-static"' -o /kube-applier . && \
diff --git a/kube/client.go b/kube/client.go
index 4f3714dc..4ca231ac 100644
--- a/kube/client.go
+++ b/kube/client.go
@@ -36,7 +36,6 @@ var execCommand = exec.Command
 //todo(catalin-ilea) Add core/v1/Secret when we plug in strongbox
 var pruneWhitelist = []string{
 	"apps/v1/DaemonSet",
-	"apps/v1beta1/DaemonSet",
 	"apps/v1/Deployment",
 	"apps/v1/StatefulSet",
 	"autoscaling/v1/HorizontalPodAutoscaler",
@@ -61,8 +60,7 @@ const (
 
 // ClientInterface allows for mocking out the functionality of Client when testing the full process of an apply run.
 type ClientInterface interface {
-	Apply(path, namespace string, dryRun, prune bool) (string, string, error)
-	StrictApply(path, namespace string, dryRun, prune bool) (string, string, error)
+	Apply(path, namespace string, dryRun, prune, strict, kustomize bool) (string, string, error)
 	CheckVersion() error
 	GetNamespaceStatus(namespace string) (AutomaticDeploymentOption, error)
 	GetNamespaceUserSecretName(namespace, username string) (string, error)
@@ -163,51 +161,73 @@ func isCompatible(clientMajor, clientMinor, serverMajor, serverMinor string) err
 	return nil
 }
 
-func prepareApplyArgs(path, namespace, label string, dryRun, prune bool) []string {
-	args := []string{"kubectl", "apply", fmt.Sprintf("--dry-run=%t", dryRun), "-R", "-f", path, fmt.Sprintf("-l %s!=%s", label, Off), "-n", namespace}
+// Apply attempts to "kubectl apply" the files located at path. It returns the
+// full apply command and its output.
+//
+// strict - attempt to "kubectl apply" the files located at path using a
+//          `kube-applier` service account under the given namespace.
+//          `kube-applier` service account must exist for the given namespace and
+//          must contain a secret that include token and ca.cert.  It returns the
+//          full apply command and its output.
+//
+// kustomize - Do a `kuztomize build` on the path before piping to `kubectl
+//             apply`, set to if there is a `kustomization.yaml` found in the path
+func (c *Client) Apply(path, namespace string, dryRun, prune, strict, kustomize bool) (string, string, error) {
+	var args []string
+
+	if kustomize {
+		args = []string{"kubectl", "apply", fmt.Sprintf("--dry-run=%t", dryRun), "-f", "-", fmt.Sprintf("-l %s!=%s", c.Label, Off), "-n", namespace}
+	} else {
+		args = []string{"kubectl", "apply", fmt.Sprintf("--dry-run=%t", dryRun), "-R", "-f", path, fmt.Sprintf("-l %s!=%s", c.Label, Off), "-n", namespace}
+	}
+
 	if prune {
 		args = append(args, "--prune")
 		for _, w := range pruneWhitelist {
 			args = append(args, "--prune-whitelist="+w)
 		}
 	}
-	return args
-}
-
-func executeApply(args []string) (string, string, error) {
-	cmd := strings.Join(args, " ")
-	stdout, err := execCommand(args[0], args[1:]...).CombinedOutput()
-	if err != nil {
-		err = errors.Wrap(err, "kubectl apply command failed")
-	}
-	return cmd, string(stdout), err
-}
 
-// Apply attempts to "kubectl apply" the file located at path.
-// It returns the full apply command and its output.
-func (c *Client) Apply(path, namespace string, dryRun, prune bool) (string, string, error) {
-	args := prepareApplyArgs(path, namespace, c.Label, dryRun, prune)
-	if c.Server != "" {
+	if strict {
+		tempKubeConfigFilepath, tempCertFilepath, err := c.CreateTempConfig(namespace, "kube-applier")
+		if err != nil {
+			return "", "", fmt.Errorf("error creating temp config: %v", err)
+		}
+		defer func() { os.Remove(tempKubeConfigFilepath); os.Remove(tempCertFilepath) }()
+		args = append(args, fmt.Sprintf("--kubeconfig=%s", tempKubeConfigFilepath))
+	} else if c.Server != "" {
 		args = append(args, fmt.Sprintf("--kubeconfig=%s", kubeconfigFilePath))
 	}
 
-	return executeApply(args)
-}
+	kubectlCmd := exec.Command(args[0], args[1:]...)
+
+	var out []byte
+	var err error
+	var cmdStr string
 
-// StrictApply will attempt to "kubectl apply" the file located at path using a `kube-applier` service account under the given namespace.
-// `kube-applier` service account must exist for the given namespace and must contain a secret that include token and ca.cert.
-// It returns the full apply command and its output.
-func (c *Client) StrictApply(path, namespace string, dryRun, prune bool) (string, string, error) {
-	args := prepareApplyArgs(path, namespace, c.Label, dryRun, prune)
+	if kustomize {
+		cmdStr = "kustomize build " + path + " | " + strings.Join(args, " ")
+		kustomizeCmd := exec.Command("kustomize", "build", path)
+		pipe, err := kustomizeCmd.StdoutPipe()
+		if err != nil {
+			return cmdStr, "", err
+		}
+		kubectlCmd.Stdin = pipe
+
+		err = kustomizeCmd.Start()
+		if err != nil {
+			return cmdStr, "", err
+		}
+	} else {
+		cmdStr = strings.Join(args, " ")
+	}
 
-	tempKubeConfigFilepath, tempCertFilepath, err := c.CreateTempConfig(namespace, "kube-applier")
+	out, err = kubectlCmd.CombinedOutput()
 	if err != nil {
-		return "", "", fmt.Errorf("error creating temp config: %v", err)
+		return cmdStr, string(out), err
 	}
-	defer func() { os.Remove(tempKubeConfigFilepath); os.Remove(tempCertFilepath) }()
-	args = append(args, fmt.Sprintf("--kubeconfig=%s", tempKubeConfigFilepath))
 
-	return executeApply(args)
+	return cmdStr, string(out), err
 }
 
 // GetNamespaceStatus returns the AutmaticDeployment label for the given namespace
diff --git a/kube/client_test.go b/kube/client_test.go
index 59276553..16fa150e 100644
--- a/kube/client_test.go
+++ b/kube/client_test.go
@@ -163,20 +163,3 @@ func TestGetUserDataFromSecret(t *testing.T) {
 		t.Fatal("Got unexpected cert")
 	}
 }
-
-func TestPrepareApplyArgsPrune(t *testing.T) {
-	assert := assert.New(t)
-
-	// Prune == false
-	expected := []string{"kubectl", "apply", "--dry-run=false", "-R", "-f", "/path", "-l autoDeployment!=off", "-n", "namespace"}
-	actual := prepareApplyArgs("/path", "namespace", "autoDeployment", false, false)
-	assert.Equal(expected, actual)
-
-	// Prune == true
-	expected = append(expected, "--prune")
-	for _, w := range pruneWhitelist {
-		expected = append(expected, "--prune-whitelist="+w)
-	}
-	actual = prepareApplyArgs("/path", "namespace", "autoDeployment", false, true)
-	assert.Equal(expected, actual)
-}
diff --git a/kube/mock_client.go b/kube/mock_client.go
index 3703c418..31da9ab9 100644
--- a/kube/mock_client.go
+++ b/kube/mock_client.go
@@ -1,5 +1,5 @@
 // Code generated by MockGen. DO NOT EDIT.
-// Source: client.go
+// Source: kube/client.go
 
 // Package kube is a generated GoMock package.
 package kube
@@ -33,8 +33,8 @@ func (m *MockClientInterface) EXPECT() *MockClientInterfaceMockRecorder {
 }
 
 // Apply mocks base method
-func (m *MockClientInterface) Apply(path, namespace string, dryRun, prune bool) (string, string, error) {
-	ret := m.ctrl.Call(m, "Apply", path, namespace, dryRun, prune)
+func (m *MockClientInterface) Apply(path, namespace string, dryRun, prune, strict, kustomize bool) (string, string, error) {
+	ret := m.ctrl.Call(m, "Apply", path, namespace, dryRun, prune, strict, kustomize)
 	ret0, _ := ret[0].(string)
 	ret1, _ := ret[1].(string)
 	ret2, _ := ret[2].(error)
@@ -42,22 +42,8 @@ func (m *MockClientInterface) Apply(path, namespace string, dryRun, prune bool)
 }
 
 // Apply indicates an expected call of Apply
-func (mr *MockClientInterfaceMockRecorder) Apply(path, namespace, dryRun, prune interface{}) *gomock.Call {
-	return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "Apply", reflect.TypeOf((*MockClientInterface)(nil).Apply), path, namespace, dryRun, prune)
-}
-
-// StrictApply mocks base method
-func (m *MockClientInterface) StrictApply(path, namespace string, dryRun, prune bool) (string, string, error) {
-	ret := m.ctrl.Call(m, "StrictApply", path, namespace, dryRun, prune)
-	ret0, _ := ret[0].(string)
-	ret1, _ := ret[1].(string)
-	ret2, _ := ret[2].(error)
-	return ret0, ret1, ret2
-}
-
-// StrictApply indicates an expected call of StrictApply
-func (mr *MockClientInterfaceMockRecorder) StrictApply(path, namespace, dryRun, prune interface{}) *gomock.Call {
-	return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "StrictApply", reflect.TypeOf((*MockClientInterface)(nil).StrictApply), path, namespace, dryRun, prune)
+func (mr *MockClientInterfaceMockRecorder) Apply(path, namespace, dryRun, prune, strict, kustomize interface{}) *gomock.Call {
+	return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "Apply", reflect.TypeOf((*MockClientInterface)(nil).Apply), path, namespace, dryRun, prune, strict, kustomize)
 }
 
 // CheckVersion mocks base method
diff --git a/run/batch_applier.go b/run/batch_applier.go
index 74ca78c3..695356ec 100644
--- a/run/batch_applier.go
+++ b/run/batch_applier.go
@@ -60,12 +60,14 @@ func (a *BatchApplier) Apply(applyList []string) ([]ApplyAttempt, []ApplyAttempt
 		default:
 			continue
 		}
-		var cmd, output string
-		if a.StrictApply {
-			cmd, output, err = a.KubeClient.StrictApply(path, ns, a.DryRun || disabled, a.Prune)
-		} else {
-			cmd, output, err = a.KubeClient.Apply(path, ns, a.DryRun || disabled, a.Prune)
+
+		var kustomize bool
+		if _, err := os.Stat(path + "/kustomization.yaml"); err == nil {
+			kustomize = true
 		}
+
+		var cmd, output string
+		cmd, output, err = a.KubeClient.Apply(path, ns, a.DryRun || disabled, a.Prune, a.StrictApply, kustomize)
 		success := (err == nil)
 		appliedFile := ApplyAttempt{path, cmd, output, ""}
 		if success {
diff --git a/run/batch_applier_test.go b/run/batch_applier_test.go
index 9277afd9..a28275f8 100644
--- a/run/batch_applier_test.go
+++ b/run/batch_applier_test.go
@@ -286,11 +286,11 @@ func expectCheckVersionAndReturnNil(kubeClient *kube.MockClientInterface) *gomoc
 }
 
 func expectApplyAndReturnSuccess(file, namespace string, dryRun, prune bool, kubeClient *kube.MockClientInterface) *gomock.Call {
-	return kubeClient.EXPECT().Apply(file, namespace, dryRun, prune).Times(1).Return("cmd "+file, "output "+file, nil)
+	return kubeClient.EXPECT().Apply(file, namespace, dryRun, prune, false, false).Times(1).Return("cmd "+file, "output "+file, nil)
 }
 
 func expectApplyAndReturnFailure(file, namespace string, dryRun, prune bool, kubeClient *kube.MockClientInterface) *gomock.Call {
-	return kubeClient.EXPECT().Apply(file, namespace, dryRun, prune).Times(1).Return("cmd "+file, "output "+file, fmt.Errorf("error "+file))
+	return kubeClient.EXPECT().Apply(file, namespace, dryRun, prune, false, false).Times(1).Return("cmd "+file, "output "+file, fmt.Errorf("error "+file))
 }
 
 func expectGetNamespaceStatusAndReturn(ret kube.AutomaticDeploymentOption, namespace string, kubeClient *kube.MockClientInterface) *gomock.Call {