diff --git a/cmd/ninja/cmd/plugin.go b/cmd/ninja/cmd/plugin.go
index 240977c..9524cff 100644
--- a/cmd/ninja/cmd/plugin.go
+++ b/cmd/ninja/cmd/plugin.go
@@ -325,6 +325,18 @@ func newPluginPublishCmd() *cobra.Command {
 				fmt.Fprintln(os.Stderr, "  (run `git rm --cached <file>` to drop)")
 			}
 
+			// `git archive` does not recurse into submodules, so any submodule
+			// paths will appear as empty directories in the tarball. Detect via
+			// .gitmodules so this works even for submodules that haven't been
+			// initialised yet.
+			if paths := submodulePaths("."); len(paths) > 0 {
+				fmt.Fprintln(os.Stderr, "warning: this repo has submodules; git archive will ship them as empty directories:")
+				for _, p := range paths {
+					fmt.Fprintln(os.Stderr, "  "+p)
+				}
+				fmt.Fprintln(os.Stderr, "  (vendor the contents or pack them separately if the plugin depends on them)")
+			}
+
 			archiveBytes, err := archive.BuildSourceArchive(".")
 			if err != nil {
 				return fmt.Errorf("build archive: %w", err)
@@ -577,6 +589,27 @@ func checkRepoHasHEAD(repoDir string) error {
 	return nil
 }
 
+// submodulePaths returns the configured submodule paths from .gitmodules.
+// Reading the file directly (rather than running `git submodule status`) means
+// we detect submodules that have been declared but not yet initialised.
+func submodulePaths(repoDir string) []string {
+	cmd := exec.Command("git", "config", "--file", ".gitmodules", "--get-regexp", `submodule\..*\.path`)
+	cmd.Dir = repoDir
+	out, err := cmd.Output()
+	if err != nil {
+		return nil
+	}
+	var paths []string
+	for _, line := range strings.Split(strings.TrimSpace(string(out)), "\n") {
+		// each line is "submodule.<name>.path <path>"
+		fields := strings.Fields(line)
+		if len(fields) >= 2 {
+			paths = append(paths, fields[len(fields)-1])
+		}
+	}
+	return paths
+}
+
 func upsertPluginMod(scope, name, kind string, categories []string) error {
 	const file = "plugin.mod"
 	existing, _ := os.ReadFile(file)