diff --git a/crate_universe/src/cli/generate.rs b/crate_universe/src/cli/generate.rs
index 4ec2638bb4..c7a3105528 100644
--- a/crate_universe/src/cli/generate.rs
+++ b/crate_universe/src/cli/generate.rs
@@ -119,9 +119,12 @@ pub fn generate(opt: GenerateOptions) -> Result<()> {
             // Write the outputs to disk
             write_outputs(normalized_outputs, opt.dry_run)?;
 
+            let splicing_manifest = SplicingManifest::try_from_path(&opt.splicing_manifest)?;
+
             write_paths_to_track(
                 &opt.paths_to_track,
                 &opt.warnings_output_path,
+                splicing_manifest.manifests.keys(),
                 context
                     .crates
                     .values()
@@ -164,9 +167,12 @@ pub fn generate(opt: GenerateOptions) -> Result<()> {
         &opt.nonhermetic_root_bazel_workspace_dir,
     )?;
 
+    let splicing_manifest = SplicingManifest::try_from_path(&opt.splicing_manifest)?;
+
     write_paths_to_track(
         &opt.paths_to_track,
         &opt.warnings_output_path,
+        splicing_manifest.manifests.keys(),
         annotations.lockfile.crates.values(),
         cargo_lockfile.patch.unused.iter(),
     )?;
@@ -189,8 +195,6 @@ pub fn generate(opt: GenerateOptions) -> Result<()> {
 
     // Ensure Bazel lockfiles are written to disk so future generations can be short-circuited.
     if let Some(lockfile) = opt.lockfile {
-        let splicing_manifest = SplicingManifest::try_from_path(&opt.splicing_manifest)?;
-
         let lock_content =
             lock_context(context, &config, &splicing_manifest, &cargo_bin, rustc_bin)?;
 
@@ -220,10 +224,12 @@ fn update_cargo_lockfile(path: &Path, cargo_lockfile: Lockfile) -> Result<()> {
 fn write_paths_to_track<
     'a,
     SourceAnnotations: Iterator<Item = &'a SourceAnnotation>,
+    Paths: Iterator<Item = &'a Utf8PathBuf>,
     UnusedPatches: Iterator<Item = &'a cargo_lock::Dependency>,
 >(
     output_file: &Path,
     warnings_output_path: &Path,
+    manifests: Paths,
     source_annotations: SourceAnnotations,
     unused_patches: UnusedPatches,
 ) -> Result<()> {
@@ -235,6 +241,7 @@ fn write_paths_to_track<
                 None
             }
         })
+        .chain(manifests)
         .collect();
     std::fs::write(
         output_file,