diff --git a/ci/priv-integration.sh b/ci/priv-integration.sh
index 41b95520..8a1b6e42 100755
--- a/ci/priv-integration.sh
+++ b/ci/priv-integration.sh
@@ -29,8 +29,14 @@ for img in "${image}"; do
     ostree-ext-cli container image deploy --sysroot "${sysroot}" \
         --stateroot "${stateroot}" --imgref ostree-unverified-registry:"${img}"
     ostree admin --sysroot="${sysroot}" status
+    initial_refs=$(ostree --repo="${sysroot}/ostree/repo" refs | wc -l)
     ostree-ext-cli container image remove --repo "${sysroot}/ostree/repo" registry:"${img}"
+    pruned_refs=$(ostree --repo="${sysroot}/ostree/repo" refs | wc -l)
+    # Removing the image should only drop the image reference, not its layers
+    test "$(($initial_refs - 1))" = "$pruned_refs"
     ostree admin --sysroot="${sysroot}" undeploy 0
+    # TODO: when we fold together ostree and ostree-ext, automatically prune layers
+    ostree-ext-cli container image prune-layers --repo="${sysroot}/ostree/repo"
     ostree --repo="${sysroot}/ostree/repo" refs > refs.txt
     if test "$(wc -l < refs.txt)" -ne 0; then
         echo "found refs"
diff --git a/lib/src/cli.rs b/lib/src/cli.rs
index 17de33c5..e76a9e38 100644
--- a/lib/src/cli.rs
+++ b/lib/src/cli.rs
@@ -252,6 +252,13 @@ pub(crate) enum ContainerImageOpts {
         skip_gc: bool,
     },
 
+    /// Garbage collect unreferenced image layer references.
+    PruneLayers {
+        /// Path to the repository
+        #[clap(long, value_parser)]
+        repo: Utf8PathBuf,
+    },
+
     /// Perform initial deployment for a container image
     Deploy {
         /// Path to the system root
@@ -777,6 +784,12 @@ where
                     }
                     Ok(())
                 }
+                ContainerImageOpts::PruneLayers { repo } => {
+                    let repo = parse_repo(&repo)?;
+                    let nlayers = crate::container::store::gc_image_layers(&repo)?;
+                    println!("Removed layers: {nlayers}");
+                    Ok(())
+                }
                 ContainerImageOpts::Copy {
                     src_repo,
                     dest_repo,
diff --git a/lib/src/container/store.rs b/lib/src/container/store.rs
index d6315c54..e58a9b77 100644
--- a/lib/src/container/store.rs
+++ b/lib/src/container/store.rs
@@ -983,6 +983,40 @@ pub async fn copy(
     Ok(())
 }
 
+/// Iterate over deployment commits, returning the manifests from
+/// commits which point to a container image.
+fn list_container_deployment_manifests(
+    repo: &ostree::Repo,
+    cancellable: Option<&gio::Cancellable>,
+) -> Result<Vec<ImageManifest>> {
+    let commits = repo
+        .list_refs_ext(
+            Some("ostree/0"),
+            ostree::RepoListRefsExtFlags::empty(),
+            cancellable,
+        )?
+        .into_iter()
+        .chain(repo.list_refs_ext(
+            Some("ostree/1"),
+            ostree::RepoListRefsExtFlags::empty(),
+            cancellable,
+        )?)
+        .map(|v| v.1);
+    let mut r = Vec::new();
+    for commit in commits {
+        let commit_obj = repo.load_commit(&commit)?.0;
+        let commit_meta = &glib::VariantDict::new(Some(&commit_obj.child_value(0)));
+        if commit_meta
+            .lookup::<String>(META_MANIFEST_DIGEST)?
+            .is_some()
+        {
+            let manifest = manifest_data_from_commitmeta(commit_meta)?.0;
+            r.push(manifest);
+        }
+    }
+    Ok(r)
+}
+
 /// Garbage collect unused image layer references.
 ///
 /// This function assumes no transaction is active on the repository.
@@ -998,11 +1032,13 @@ fn gc_image_layers_impl(
     cancellable: Option<&gio::Cancellable>,
 ) -> Result<u32> {
     let all_images = list_images(repo)?;
+    let deployment_commits = list_container_deployment_manifests(repo, cancellable)?;
     let all_manifests = all_images
         .into_iter()
         .map(|img| {
             ImageReference::try_from(img.as_str()).and_then(|ir| manifest_for_image(repo, &ir))
         })
+        .chain(deployment_commits.into_iter().map(Ok))
         .collect::<Result<Vec<_>>>()?;
     let mut referenced_layers = BTreeSet::new();
     for m in all_manifests.iter() {