diff --git a/terraform/graph_builder.go b/terraform/graph_builder.go
index 7963bcbf4..793dc904c 100644
--- a/terraform/graph_builder.go
+++ b/terraform/graph_builder.go
@@ -136,9 +136,6 @@ func (b *BuiltinGraphBuilder) Steps(path []string) []GraphTransformer {
 
 		// Make sure all the connections that are proxies are connected through
 		&ProxyTransformer{},
-
-		// Make sure we have a single root
-		&RootTransformer{},
 	}
 
 	// If we're on the root path, then we do a bunch of other stuff.
@@ -170,17 +167,15 @@ func (b *BuiltinGraphBuilder) Steps(path []string) []GraphTransformer {
 			&CloseProviderTransformer{},
 			&CloseProvisionerTransformer{},
 
-			// Make sure we have a single root after the above changes.
-			// This is the 2nd root transformer. In practice this shouldn't
-			// actually matter as the RootTransformer is idempotent.
-			&RootTransformer{},
-
 			// Perform the transitive reduction to make our graph a bit
 			// more sane if possible (it usually is possible).
 			&TransitiveReductionTransformer{},
 		)
 	}
 
+	// Make sure we have a single root
+	steps = append(steps, &RootTransformer{})
+
 	// Remove nils
 	for i, s := range steps {
 		if s == nil {
diff --git a/terraform/transform_provisioner.go b/terraform/transform_provisioner.go
index a99fe48b0..dc8513f95 100644
--- a/terraform/transform_provisioner.go
+++ b/terraform/transform_provisioner.go
@@ -97,15 +97,38 @@ type MissingProvisionerTransformer struct {
 }
 
 func (t *MissingProvisionerTransformer) Transform(g *Graph) error {
+	// Create a set of our supported provisioners
+	supported := make(map[string]struct{}, len(t.Provisioners))
+	for _, v := range t.Provisioners {
+		supported[v] = struct{}{}
+	}
+
+	// Get the map of provisioners we already have in our graph
 	m := provisionerVertexMap(g)
-	for _, p := range t.Provisioners {
-		if _, ok := m[p]; ok {
-			// This provisioner already exists as a configured node
+
+	// Go through all the provisioner consumers and make sure we add
+	// that provisioner if it is missing.
+	for _, v := range g.Vertices() {
+		pv, ok := v.(GraphNodeProvisionerConsumer)
+		if !ok {
 			continue
 		}
 
-		// Add our own missing provisioner node to the graph
-		g.Add(&graphNodeMissingProvisioner{ProvisionerNameValue: p})
+		for _, p := range pv.ProvisionedBy() {
+			if _, ok := m[p]; ok {
+				// This provisioner already exists as a configure node
+				continue
+			}
+
+			if _, ok := supported[p]; !ok {
+				// If we don't support the provisioner type, skip it.
+				// Validation later will catch this as an error.
+				continue
+			}
+
+			// Add our own missing provisioner node to the graph
+			m[p] = g.Add(&graphNodeMissingProvisioner{ProvisionerNameValue: p})
+		}
 	}
 
 	return nil
diff --git a/terraform/transform_provisioner_test.go b/terraform/transform_provisioner_test.go
index ea5faff77..823835372 100644
--- a/terraform/transform_provisioner_test.go
+++ b/terraform/transform_provisioner_test.go
@@ -101,7 +101,6 @@ func TestGraphNodeMissingProvisioner_ProvisionerName(t *testing.T) {
 
 const testTransformMissingProvisionerBasicStr = `
 aws_instance.web
-provisioner.foo
 provisioner.shell (close)
   aws_instance.web
 `