diff --git a/libcontainer/cgroups/fs/apply_raw.go b/libcontainer/cgroups/fs/apply_raw.go
index c67c55acd..8eb71b4dd 100644
--- a/libcontainer/cgroups/fs/apply_raw.go
+++ b/libcontainer/cgroups/fs/apply_raw.go
@@ -171,16 +171,24 @@ func (m *Manager) GetStats() (*cgroups.Stats, error) {
 }
 
 func (m *Manager) Set(container *configs.Config) error {
-	for name, path := range m.Paths {
+	for _, sys := range subsystems {
 		// We can't set this here, because after being applied, memcg doesn't
 		// allow a non-empty cgroup from having its limits changed.
-		if name == "memory" {
+		if sys.Name() == "memory" {
 			continue
 		}
-		sys, err := subsystems.Get(name)
-		if err == errSubsystemDoesNotExist || !cgroups.PathExists(path) {
-			continue
+
+		// Generate fake cgroup data.
+		d, err := getCgroupData(container.Cgroups, -1)
+		if err != nil {
+			return err
 		}
+		// Get the path, but don't error out if the cgroup wasn't found.
+		path, err := d.path(sys.Name())
+		if err != nil && !cgroups.IsNotFound(err) {
+			return err
+		}
+
 		if err := sys.Set(path, container.Cgroups); err != nil {
 			return err
 		}
diff --git a/libcontainer/cgroups/systemd/apply_systemd.go b/libcontainer/cgroups/systemd/apply_systemd.go
index 952820e62..b943e9dae 100644
--- a/libcontainer/cgroups/systemd/apply_systemd.go
+++ b/libcontainer/cgroups/systemd/apply_systemd.go
@@ -431,16 +431,19 @@ func (m *Manager) GetStats() (*cgroups.Stats, error) {
 }
 
 func (m *Manager) Set(container *configs.Config) error {
-	for name, path := range m.Paths {
+	for _, sys := range subsystems {
 		// We can't set this here, because after being applied, memcg doesn't
 		// allow a non-empty cgroup from having its limits changed.
-		if name == "memory" {
+		if sys.Name() == "memory" {
 			continue
 		}
-		sys, err := subsystems.Get(name)
-		if err == errSubsystemDoesNotExist || !cgroups.PathExists(path) {
-			continue
+
+		// Get the subsystem path, but don't error out for not found cgroups.
+		path, err := getSubsystemPath(container.Cgroups, sys.Name())
+		if err != nil && !cgroups.IsNotFound(err) {
+			return err
 		}
+
 		if err := sys.Set(path, container.Cgroups); err != nil {
 			return err
 		}