diff --git a/tools/container/runtime/containerd/containerd.go b/tools/container/runtime/containerd/containerd.go
index 6a5df5ad..14b0a5d3 100644
--- a/tools/container/runtime/containerd/containerd.go
+++ b/tools/container/runtime/containerd/containerd.go
@@ -25,6 +25,7 @@ import (
 
 	"github.com/NVIDIA/nvidia-container-toolkit/pkg/config/engine"
 	"github.com/NVIDIA/nvidia-container-toolkit/pkg/config/engine/containerd"
+	"github.com/NVIDIA/nvidia-container-toolkit/pkg/config/toml"
 	"github.com/NVIDIA/nvidia-container-toolkit/tools/container"
 )
 
@@ -116,7 +117,12 @@ func Cleanup(c *cli.Context, o *container.Options, co *Options) error {
 
 	cfg, err := containerd.New(
 		containerd.WithPath(o.Config),
-		containerd.WithConfigSource(containerd.CommandLineSource(o.HostRootMount)),
+		containerd.WithConfigSource(
+			toml.LoadFirst(
+				containerd.CommandLineSource(o.HostRootMount),
+				toml.FromFile(o.Config),
+			),
+		),
 		containerd.WithRuntimeType(co.runtimeType),
 		containerd.WithUseLegacyConfig(co.useLegacyConfig),
 		containerd.WithContainerAnnotations(co.containerAnnotationsFromCDIPrefixes()...),
diff --git a/tools/container/runtime/crio/crio.go b/tools/container/runtime/crio/crio.go
index e3fa77f6..68b36f45 100644
--- a/tools/container/runtime/crio/crio.go
+++ b/tools/container/runtime/crio/crio.go
@@ -28,6 +28,7 @@ import (
 	"github.com/NVIDIA/nvidia-container-toolkit/pkg/config/engine"
 	"github.com/NVIDIA/nvidia-container-toolkit/pkg/config/engine/crio"
 	"github.com/NVIDIA/nvidia-container-toolkit/pkg/config/ocihook"
+	"github.com/NVIDIA/nvidia-container-toolkit/pkg/config/toml"
 	"github.com/NVIDIA/nvidia-container-toolkit/tools/container"
 )
 
@@ -170,7 +171,12 @@ func cleanupConfig(o *container.Options) error {
 
 	cfg, err := crio.New(
 		crio.WithPath(o.Config),
-		crio.WithConfigSource(crio.CommandLineSource(o.HostRootMount)),
+		crio.WithConfigSource(
+			toml.LoadFirst(
+				crio.CommandLineSource(o.HostRootMount),
+				toml.FromFile(o.Config),
+			),
+		),
 	)
 	if err != nil {
 		return fmt.Errorf("unable to load config: %v", err)