diff --git a/builtin/rm.c b/builtin/rm.c
index 7f15a3d7f8..452170a3ab 100644
--- a/builtin/rm.c
+++ b/builtin/rm.c
@@ -59,27 +59,9 @@ static void print_error_files(struct string_list *files_list,
 	}
 }
 
-static void error_removing_concrete_submodules(struct string_list *files, int *errs)
-{
-	print_error_files(files,
-			  Q_("the following submodule (or one of its nested "
-			     "submodules)\n"
-			     "uses a .git directory:",
-			     "the following submodules (or one of their nested "
-			     "submodules)\n"
-			     "use a .git directory:", files->nr),
-			  _("\n(use 'rm -rf' if you really want to remove "
-			    "it including all of its history)"),
-			  errs);
-	string_list_clear(files, 0);
-}
-
-static int check_submodules_use_gitfiles(void)
+static void submodules_absorb_gitdir_if_needed(const char *prefix)
 {
 	int i;
-	int errs = 0;
-	struct string_list files = STRING_LIST_INIT_NODUP;
-
 	for (i = 0; i < list.nr; i++) {
 		const char *name = list.entry[i].name;
 		int pos;
@@ -99,12 +81,9 @@ static int check_submodules_use_gitfiles(void)
 			continue;
 
 		if (!submodule_uses_gitfile(name))
-			string_list_append(&files, name);
+			absorb_git_dir_into_superproject(prefix, name,
+				ABSORB_GITDIR_RECURSE_SUBMODULES);
 	}
-
-	error_removing_concrete_submodules(&files, &errs);
-
-	return errs;
 }
 
 static int check_local_mod(struct object_id *head, int index_only)
@@ -120,7 +99,6 @@ static int check_local_mod(struct object_id *head, int index_only)
 	int errs = 0;
 	struct string_list files_staged = STRING_LIST_INIT_NODUP;
 	struct string_list files_cached = STRING_LIST_INIT_NODUP;
-	struct string_list files_submodule = STRING_LIST_INIT_NODUP;
 	struct string_list files_local = STRING_LIST_INIT_NODUP;
 
 	no_head = is_null_oid(head);
@@ -187,7 +165,9 @@ static int check_local_mod(struct object_id *head, int index_only)
 		 */
 		if (ce_match_stat(ce, &st, 0) ||
 		    (S_ISGITLINK(ce->ce_mode) &&
-		     !ok_to_remove_submodule(ce->name)))
+		     bad_to_remove_submodule(ce->name,
+				SUBMODULE_REMOVAL_DIE_ON_ERROR |
+				SUBMODULE_REMOVAL_IGNORE_IGNORED_UNTRACKED)))
 			local_changes = 1;
 
 		/*
@@ -217,13 +197,8 @@ static int check_local_mod(struct object_id *head, int index_only)
 		else if (!index_only) {
 			if (staged_changes)
 				string_list_append(&files_cached, name);
-			if (local_changes) {
-				if (S_ISGITLINK(ce->ce_mode) &&
-				    !submodule_uses_gitfile(name))
-					string_list_append(&files_submodule, name);
-				else
-					string_list_append(&files_local, name);
-			}
+			if (local_changes)
+				string_list_append(&files_local, name);
 		}
 	}
 	print_error_files(&files_staged,
@@ -245,8 +220,6 @@ static int check_local_mod(struct object_id *head, int index_only)
 			  &errs);
 	string_list_clear(&files_cached, 0);
 
-	error_removing_concrete_submodules(&files_submodule, &errs);
-
 	print_error_files(&files_local,
 			  Q_("the following file has local modifications:",
 			     "the following files have local modifications:",
@@ -340,6 +313,9 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			exit(0);
 	}
 
+	if (!index_only)
+		submodules_absorb_gitdir_if_needed(prefix);
+
 	/*
 	 * If not forced, the file, the index and the HEAD (if exists)
 	 * must match; but the file can already been removed, since
@@ -356,9 +332,6 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			oidclr(&oid);
 		if (check_local_mod(&oid, index_only))
 			exit(1);
-	} else if (!index_only) {
-		if (check_submodules_use_gitfiles())
-			exit(1);
 	}
 
 	/*
@@ -387,32 +360,20 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	 */
 	if (!index_only) {
 		int removed = 0, gitmodules_modified = 0;
-		struct strbuf buf = STRBUF_INIT;
 		for (i = 0; i < list.nr; i++) {
 			const char *path = list.entry[i].name;
 			if (list.entry[i].is_submodule) {
-				if (is_empty_dir(path)) {
-					if (!rmdir(path)) {
-						removed = 1;
-						if (!remove_path_from_gitmodules(path))
-							gitmodules_modified = 1;
-						continue;
-					}
-				} else {
-					strbuf_reset(&buf);
-					strbuf_addstr(&buf, path);
-					if (!remove_dir_recursively(&buf, 0)) {
-						removed = 1;
-						if (!remove_path_from_gitmodules(path))
-							gitmodules_modified = 1;
-						strbuf_release(&buf);
-						continue;
-					} else if (!file_exists(path))
-						/* Submodule was removed by user */
-						if (!remove_path_from_gitmodules(path))
-							gitmodules_modified = 1;
-					/* Fallthrough and let remove_path() fail. */
-				}
+				struct strbuf buf = STRBUF_INIT;
+
+				strbuf_addstr(&buf, path);
+				if (remove_dir_recursively(&buf, 0))
+					die(_("could not remove '%s'"), path);
+				strbuf_release(&buf);
+
+				removed = 1;
+				if (!remove_path_from_gitmodules(path))
+					gitmodules_modified = 1;
+				continue;
 			}
 			if (!remove_path(path)) {
 				removed = 1;
@@ -421,7 +382,6 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			if (!removed)
 				die_errno("git rm: '%s'", path);
 		}
-		strbuf_release(&buf);
 		if (gitmodules_modified)
 			stage_updated_gitmodules();
 	}
diff --git a/submodule.c b/submodule.c
index f8fee3dfdd..11ff11ed89 100644
--- a/submodule.c
+++ b/submodule.c
@@ -1143,45 +1143,64 @@ int submodule_uses_gitfile(const char *path)
 	return 1;
 }
 
-int ok_to_remove_submodule(const char *path)
+/*
+ * Check if it is a bad idea to remove a submodule, i.e. if we'd lose data
+ * when doing so.
+ *
+ * Return 1 if we'd lose data, return 0 if the removal is fine,
+ * and negative values for errors.
+ */
+int bad_to_remove_submodule(const char *path, unsigned flags)
 {
 	ssize_t len;
 	struct child_process cp = CHILD_PROCESS_INIT;
-	const char *argv[] = {
-		"status",
-		"--porcelain",
-		"-u",
-		"--ignore-submodules=none",
-		NULL,
-	};
 	struct strbuf buf = STRBUF_INIT;
-	int ok_to_remove = 1;
+	int ret = 0;
 
 	if (!file_exists(path) || is_empty_dir(path))
-		return 1;
-
-	if (!submodule_uses_gitfile(path))
 		return 0;
 
-	cp.argv = argv;
+	if (!submodule_uses_gitfile(path))
+		return 1;
+
+	argv_array_pushl(&cp.args, "status", "--porcelain",
+				   "--ignore-submodules=none", NULL);
+
+	if (flags & SUBMODULE_REMOVAL_IGNORE_UNTRACKED)
+		argv_array_push(&cp.args, "-uno");
+	else
+		argv_array_push(&cp.args, "-uall");
+
+	if (!(flags & SUBMODULE_REMOVAL_IGNORE_IGNORED_UNTRACKED))
+		argv_array_push(&cp.args, "--ignored");
+
 	prepare_submodule_repo_env(&cp.env_array);
 	cp.git_cmd = 1;
 	cp.no_stdin = 1;
 	cp.out = -1;
 	cp.dir = path;
-	if (start_command(&cp))
-		die("Could not run 'git status --porcelain -uall --ignore-submodules=none' in submodule %s", path);
+	if (start_command(&cp)) {
+		if (flags & SUBMODULE_REMOVAL_DIE_ON_ERROR)
+			die(_("could not start 'git status in submodule '%s'"),
+				path);
+		ret = -1;
+		goto out;
+	}
 
 	len = strbuf_read(&buf, cp.out, 1024);
 	if (len > 2)
-		ok_to_remove = 0;
+		ret = 1;
 	close(cp.out);
 
-	if (finish_command(&cp))
-		die("'git status --porcelain -uall --ignore-submodules=none' failed in submodule %s", path);
-
+	if (finish_command(&cp)) {
+		if (flags & SUBMODULE_REMOVAL_DIE_ON_ERROR)
+			die(_("could not run 'git status in submodule '%s'"),
+				path);
+		ret = -1;
+	}
+out:
 	strbuf_release(&buf);
-	return ok_to_remove;
+	return ret;
 }
 
 static int find_first_merges(struct object_array *result, const char *path,
diff --git a/submodule.h b/submodule.h
index 1ccaf0e6ba..b7fe4d2027 100644
--- a/submodule.h
+++ b/submodule.h
@@ -30,55 +30,63 @@ struct submodule_update_strategy {
 };
 #define SUBMODULE_UPDATE_STRATEGY_INIT {SM_UPDATE_UNSPECIFIED, NULL}
 
-int is_staging_gitmodules_ok(void);
-int update_path_in_gitmodules(const char *oldpath, const char *newpath);
-int remove_path_from_gitmodules(const char *path);
-void stage_updated_gitmodules(void);
-void set_diffopt_flags_from_submodule_config(struct diff_options *diffopt,
+extern int is_staging_gitmodules_ok(void);
+extern int update_path_in_gitmodules(const char *oldpath, const char *newpath);
+extern int remove_path_from_gitmodules(const char *path);
+extern void stage_updated_gitmodules(void);
+extern void set_diffopt_flags_from_submodule_config(struct diff_options *,
 		const char *path);
-int submodule_config(const char *var, const char *value, void *cb);
-void gitmodules_config(void);
+extern int submodule_config(const char *var, const char *value, void *cb);
+extern void gitmodules_config(void);
 extern void gitmodules_config_sha1(const unsigned char *commit_sha1);
 extern int is_submodule_initialized(const char *path);
 extern int is_submodule_populated(const char *path);
-int parse_submodule_update_strategy(const char *value,
+extern int parse_submodule_update_strategy(const char *value,
 		struct submodule_update_strategy *dst);
-const char *submodule_strategy_to_string(const struct submodule_update_strategy *s);
-void handle_ignore_submodules_arg(struct diff_options *diffopt, const char *);
-void show_submodule_summary(FILE *f, const char *path,
+extern const char *submodule_strategy_to_string(const struct submodule_update_strategy *s);
+extern void handle_ignore_submodules_arg(struct diff_options *, const char *);
+extern void show_submodule_summary(FILE *f, const char *path,
 		const char *line_prefix,
 		struct object_id *one, struct object_id *two,
 		unsigned dirty_submodule, const char *meta,
 		const char *del, const char *add, const char *reset);
-void show_submodule_inline_diff(FILE *f, const char *path,
+extern void show_submodule_inline_diff(FILE *f, const char *path,
 		const char *line_prefix,
 		struct object_id *one, struct object_id *two,
 		unsigned dirty_submodule, const char *meta,
 		const char *del, const char *add, const char *reset,
 		const struct diff_options *opt);
-void set_config_fetch_recurse_submodules(int value);
-void check_for_new_submodule_commits(unsigned char new_sha1[20]);
-int fetch_populated_submodules(const struct argv_array *options,
+extern void set_config_fetch_recurse_submodules(int value);
+extern void check_for_new_submodule_commits(unsigned char new_sha1[20]);
+extern int fetch_populated_submodules(const struct argv_array *options,
 			       const char *prefix, int command_line_option,
 			       int quiet, int max_parallel_jobs);
-unsigned is_submodule_modified(const char *path, int ignore_untracked);
-int submodule_uses_gitfile(const char *path);
-int ok_to_remove_submodule(const char *path);
-int merge_submodule(unsigned char result[20], const char *path, const unsigned char base[20],
-		    const unsigned char a[20], const unsigned char b[20], int search);
-int find_unpushed_submodules(struct sha1_array *commits, const char *remotes_name,
-		struct string_list *needs_pushing);
+extern unsigned is_submodule_modified(const char *path, int ignore_untracked);
+extern int submodule_uses_gitfile(const char *path);
+
+#define SUBMODULE_REMOVAL_DIE_ON_ERROR (1<<0)
+#define SUBMODULE_REMOVAL_IGNORE_UNTRACKED (1<<1)
+#define SUBMODULE_REMOVAL_IGNORE_IGNORED_UNTRACKED (1<<2)
+extern int bad_to_remove_submodule(const char *path, unsigned flags);
+extern int merge_submodule(unsigned char result[20], const char *path,
+			   const unsigned char base[20],
+			   const unsigned char a[20],
+			   const unsigned char b[20], int search);
+extern int find_unpushed_submodules(struct sha1_array *commits,
+				    const char *remotes_name,
+				    struct string_list *needs_pushing);
 extern int push_unpushed_submodules(struct sha1_array *commits,
 				    const char *remotes_name,
 				    int dry_run);
-int parallel_submodules(void);
+extern void connect_work_tree_and_git_dir(const char *work_tree, const char *git_dir);
+extern int parallel_submodules(void);
 
 /*
  * Prepare the "env_array" parameter of a "struct child_process" for executing
  * a submodule by clearing any repo-specific envirionment variables, but
  * retaining any config in the environment.
  */
-void prepare_submodule_repo_env(struct argv_array *out);
+extern void prepare_submodule_repo_env(struct argv_array *out);
 
 #define ABSORB_GITDIR_RECURSE_SUBMODULES (1<<0)
 extern void absorb_git_dir_into_superproject(const char *prefix,
diff --git a/t/t3600-rm.sh b/t/t3600-rm.sh
index bcbb680651..5aa6db584c 100755
--- a/t/t3600-rm.sh
+++ b/t/t3600-rm.sh
@@ -569,26 +569,22 @@ test_expect_success 'rm of a conflicted unpopulated submodule succeeds' '
 	test_cmp expect actual
 '
 
-test_expect_success 'rm of a populated submodule with a .git directory fails even when forced' '
+test_expect_success 'rm of a populated submodule with a .git directory migrates git dir' '
 	git checkout -f master &&
 	git reset --hard &&
 	git submodule update &&
 	(cd submod &&
 		rm .git &&
 		cp -R ../.git/modules/sub .git &&
-		GIT_WORK_TREE=. git config --unset core.worktree
+		GIT_WORK_TREE=. git config --unset core.worktree &&
+		rm -r ../.git/modules/sub
 	) &&
-	test_must_fail git rm submod &&
-	test -d submod &&
-	test -d submod/.git &&
+	git rm submod 2>output.err &&
+	! test -d submod &&
+	! test -d submod/.git &&
 	git status -s -uno --ignore-submodules=none >actual &&
-	! test -s actual &&
-	test_must_fail git rm -f submod &&
-	test -d submod &&
-	test -d submod/.git &&
-	git status -s -uno --ignore-submodules=none >actual &&
-	! test -s actual &&
-	rm -rf submod
+	test -s actual &&
+	test_i18ngrep Migrating output.err
 '
 
 cat >expect.deepmodified <<EOF
@@ -667,24 +663,19 @@ test_expect_success 'rm of a populated nested submodule with a nested .git direc
 	git submodule update --recursive &&
 	(cd submod/subsubmod &&
 		rm .git &&
-		cp -R ../../.git/modules/sub/modules/sub .git &&
+		mv ../../.git/modules/sub/modules/sub .git &&
 		GIT_WORK_TREE=. git config --unset core.worktree
 	) &&
-	test_must_fail git rm submod &&
-	test -d submod &&
-	test -d submod/subsubmod/.git &&
+	git rm submod 2>output.err &&
+	! test -d submod &&
+	! test -d submod/subsubmod/.git &&
 	git status -s -uno --ignore-submodules=none >actual &&
-	! test -s actual &&
-	test_must_fail git rm -f submod &&
-	test -d submod &&
-	test -d submod/subsubmod/.git &&
-	git status -s -uno --ignore-submodules=none >actual &&
-	! test -s actual &&
-	rm -rf submod
+	test -s actual &&
+	test_i18ngrep Migrating output.err
 '
 
 test_expect_success 'checking out a commit after submodule removal needs manual updates' '
-	git commit -m "submodule removal" submod &&
+	git commit -m "submodule removal" submod .gitmodules &&
 	git checkout HEAD^ &&
 	git submodule update &&
 	git checkout -q HEAD^ &&