diff --git a/.gitignore b/.gitignore
index ffceea7d59..b59661cb88 100644
--- a/.gitignore
+++ b/.gitignore
@@ -157,6 +157,7 @@
 /git-show-ref
 /git-stage
 /git-stash
+/git-stash--helper
 /git-status
 /git-stripspace
 /git-submodule
diff --git a/Makefile b/Makefile
index d03df31c2a..f900c68e69 100644
--- a/Makefile
+++ b/Makefile
@@ -1093,6 +1093,7 @@ BUILTIN_OBJS += builtin/shortlog.o
 BUILTIN_OBJS += builtin/show-branch.o
 BUILTIN_OBJS += builtin/show-index.o
 BUILTIN_OBJS += builtin/show-ref.o
+BUILTIN_OBJS += builtin/stash--helper.o
 BUILTIN_OBJS += builtin/stripspace.o
 BUILTIN_OBJS += builtin/submodule--helper.o
 BUILTIN_OBJS += builtin/symbolic-ref.o
diff --git a/builtin.h b/builtin.h
index 99206df4bd..317bc338f7 100644
--- a/builtin.h
+++ b/builtin.h
@@ -223,6 +223,7 @@ extern int cmd_show(int argc, const char **argv, const char *prefix);
 extern int cmd_show_branch(int argc, const char **argv, const char *prefix);
 extern int cmd_show_index(int argc, const char **argv, const char *prefix);
 extern int cmd_status(int argc, const char **argv, const char *prefix);
+extern int cmd_stash__helper(int argc, const char **argv, const char *prefix);
 extern int cmd_stripspace(int argc, const char **argv, const char *prefix);
 extern int cmd_submodule__helper(int argc, const char **argv, const char *prefix);
 extern int cmd_symbolic_ref(int argc, const char **argv, const char *prefix);
diff --git a/builtin/stash--helper.c b/builtin/stash--helper.c
new file mode 100644
index 0000000000..7819dae332
--- /dev/null
+++ b/builtin/stash--helper.c
@@ -0,0 +1,452 @@
+#include "builtin.h"
+#include "config.h"
+#include "parse-options.h"
+#include "refs.h"
+#include "lockfile.h"
+#include "cache-tree.h"
+#include "unpack-trees.h"
+#include "merge-recursive.h"
+#include "argv-array.h"
+#include "run-command.h"
+#include "dir.h"
+#include "rerere.h"
+
+static const char * const git_stash_helper_usage[] = {
+	N_("git stash--helper apply [--index] [-q|--quiet] [<stash>]"),
+	NULL
+};
+
+static const char * const git_stash_helper_apply_usage[] = {
+	N_("git stash--helper apply [--index] [-q|--quiet] [<stash>]"),
+	NULL
+};
+
+static const char *ref_stash = "refs/stash";
+static struct strbuf stash_index_path = STRBUF_INIT;
+
+/*
+ * w_commit is set to the commit containing the working tree
+ * b_commit is set to the base commit
+ * i_commit is set to the commit containing the index tree
+ * u_commit is set to the commit containing the untracked files tree
+ * w_tree is set to the working tree
+ * b_tree is set to the base tree
+ * i_tree is set to the index tree
+ * u_tree is set to the untracked files tree
+ */
+
+struct stash_info {
+	struct object_id w_commit;
+	struct object_id b_commit;
+	struct object_id i_commit;
+	struct object_id u_commit;
+	struct object_id w_tree;
+	struct object_id b_tree;
+	struct object_id i_tree;
+	struct object_id u_tree;
+	struct strbuf revision;
+	int is_stash_ref;
+	int has_u;
+};
+
+static void free_stash_info(struct stash_info *info)
+{
+	strbuf_release(&info->revision);
+}
+
+static void assert_stash_like(struct stash_info *info, const char *revision)
+{
+	if (get_oidf(&info->b_commit, "%s^1", revision) ||
+	    get_oidf(&info->w_tree, "%s:", revision) ||
+	    get_oidf(&info->b_tree, "%s^1:", revision) ||
+	    get_oidf(&info->i_tree, "%s^2:", revision)) {
+		free_stash_info(info);
+		error(_("'%s' is not a stash-like commit"), revision);
+		exit(128);
+	}
+}
+
+static int get_stash_info(struct stash_info *info, int argc, const char **argv)
+{
+	int ret;
+	char *end_of_rev;
+	char *expanded_ref;
+	const char *revision;
+	const char *commit = NULL;
+	struct object_id dummy;
+	struct strbuf symbolic = STRBUF_INIT;
+
+	if (argc > 1) {
+		int i;
+		struct strbuf refs_msg = STRBUF_INIT;
+		for (i = 0; i < argc; i++)
+			strbuf_addf(&refs_msg, " '%s'", argv[i]);
+
+		fprintf_ln(stderr, _("Too many revisions specified:%s"),
+			   refs_msg.buf);
+		strbuf_release(&refs_msg);
+
+		return -1;
+	}
+
+	if (argc == 1)
+		commit = argv[0];
+
+	strbuf_init(&info->revision, 0);
+	if (!commit) {
+		if (!ref_exists(ref_stash)) {
+			free_stash_info(info);
+			fprintf_ln(stderr, _("No stash entries found."));
+			return -1;
+		}
+
+		strbuf_addf(&info->revision, "%s@{0}", ref_stash);
+	} else if (strspn(commit, "0123456789") == strlen(commit)) {
+		strbuf_addf(&info->revision, "%s@{%s}", ref_stash, commit);
+	} else {
+		strbuf_addstr(&info->revision, commit);
+	}
+
+	revision = info->revision.buf;
+
+	if (get_oid(revision, &info->w_commit)) {
+		error(_("%s is not a valid reference"), revision);
+		free_stash_info(info);
+		return -1;
+	}
+
+	assert_stash_like(info, revision);
+
+	info->has_u = !get_oidf(&info->u_tree, "%s^3:", revision);
+
+	end_of_rev = strchrnul(revision, '@');
+	strbuf_add(&symbolic, revision, end_of_rev - revision);
+
+	ret = dwim_ref(symbolic.buf, symbolic.len, &dummy, &expanded_ref);
+	strbuf_release(&symbolic);
+	switch (ret) {
+	case 0: /* Not found, but valid ref */
+		info->is_stash_ref = 0;
+		break;
+	case 1:
+		info->is_stash_ref = !strcmp(expanded_ref, ref_stash);
+		break;
+	default: /* Invalid or ambiguous */
+		free_stash_info(info);
+	}
+
+	free(expanded_ref);
+	return !(ret == 0 || ret == 1);
+}
+
+static int reset_tree(struct object_id *i_tree, int update, int reset)
+{
+	int nr_trees = 1;
+	struct unpack_trees_options opts;
+	struct tree_desc t[MAX_UNPACK_TREES];
+	struct tree *tree;
+	struct lock_file lock_file = LOCK_INIT;
+
+	read_cache_preload(NULL);
+	if (refresh_cache(REFRESH_QUIET))
+		return -1;
+
+	hold_locked_index(&lock_file, LOCK_DIE_ON_ERROR);
+
+	memset(&opts, 0, sizeof(opts));
+
+	tree = parse_tree_indirect(i_tree);
+	if (parse_tree(tree))
+		return -1;
+
+	init_tree_desc(t, tree->buffer, tree->size);
+
+	opts.head_idx = 1;
+	opts.src_index = &the_index;
+	opts.dst_index = &the_index;
+	opts.merge = 1;
+	opts.reset = reset;
+	opts.update = update;
+	opts.fn = oneway_merge;
+
+	if (unpack_trees(nr_trees, t, &opts))
+		return -1;
+
+	if (write_locked_index(&the_index, &lock_file, COMMIT_LOCK))
+		return error(_("unable to write new index file"));
+
+	return 0;
+}
+
+static int diff_tree_binary(struct strbuf *out, struct object_id *w_commit)
+{
+	struct child_process cp = CHILD_PROCESS_INIT;
+	const char *w_commit_hex = oid_to_hex(w_commit);
+
+	/*
+	 * Diff-tree would not be very hard to replace with a native function,
+	 * however it should be done together with apply_cached.
+	 */
+	cp.git_cmd = 1;
+	argv_array_pushl(&cp.args, "diff-tree", "--binary", NULL);
+	argv_array_pushf(&cp.args, "%s^2^..%s^2", w_commit_hex, w_commit_hex);
+
+	return pipe_command(&cp, NULL, 0, out, 0, NULL, 0);
+}
+
+static int apply_cached(struct strbuf *out)
+{
+	struct child_process cp = CHILD_PROCESS_INIT;
+
+	/*
+	 * Apply currently only reads either from stdin or a file, thus
+	 * apply_all_patches would have to be updated to optionally take a
+	 * buffer.
+	 */
+	cp.git_cmd = 1;
+	argv_array_pushl(&cp.args, "apply", "--cached", NULL);
+	return pipe_command(&cp, out->buf, out->len, NULL, 0, NULL, 0);
+}
+
+static int reset_head(void)
+{
+	struct child_process cp = CHILD_PROCESS_INIT;
+
+	/*
+	 * Reset is overall quite simple, however there is no current public
+	 * API for resetting.
+	 */
+	cp.git_cmd = 1;
+	argv_array_push(&cp.args, "reset");
+
+	return run_command(&cp);
+}
+
+static int get_newly_staged(struct strbuf *out, struct object_id *c_tree)
+{
+	struct child_process cp = CHILD_PROCESS_INIT;
+	const char *c_tree_hex = oid_to_hex(c_tree);
+
+	/*
+	 * diff-index is very similar to diff-tree above, and should be
+	 * converted together with update_index.
+	 */
+	cp.git_cmd = 1;
+	argv_array_pushl(&cp.args, "diff-index", "--cached", "--name-only",
+			 "--diff-filter=A", NULL);
+	argv_array_push(&cp.args, c_tree_hex);
+	return pipe_command(&cp, NULL, 0, out, 0, NULL, 0);
+}
+
+static int update_index(struct strbuf *out)
+{
+	struct child_process cp = CHILD_PROCESS_INIT;
+
+	/*
+	 * Update-index is very complicated and may need to have a public
+	 * function exposed in order to remove this forking.
+	 */
+	cp.git_cmd = 1;
+	argv_array_pushl(&cp.args, "update-index", "--add", "--stdin", NULL);
+	return pipe_command(&cp, out->buf, out->len, NULL, 0, NULL, 0);
+}
+
+static int restore_untracked(struct object_id *u_tree)
+{
+	int res;
+	struct child_process cp = CHILD_PROCESS_INIT;
+
+	/*
+	 * We need to run restore files from a given index, but without
+	 * affecting the current index, so we use GIT_INDEX_FILE with
+	 * run_command to fork processes that will not interfere.
+	 */
+	cp.git_cmd = 1;
+	argv_array_push(&cp.args, "read-tree");
+	argv_array_push(&cp.args, oid_to_hex(u_tree));
+	argv_array_pushf(&cp.env_array, "GIT_INDEX_FILE=%s",
+			 stash_index_path.buf);
+	if (run_command(&cp)) {
+		remove_path(stash_index_path.buf);
+		return -1;
+	}
+
+	child_process_init(&cp);
+	cp.git_cmd = 1;
+	argv_array_pushl(&cp.args, "checkout-index", "--all", NULL);
+	argv_array_pushf(&cp.env_array, "GIT_INDEX_FILE=%s",
+			 stash_index_path.buf);
+
+	res = run_command(&cp);
+	remove_path(stash_index_path.buf);
+	return res;
+}
+
+static int do_apply_stash(const char *prefix, struct stash_info *info,
+			  int index, int quiet)
+{
+	int ret;
+	int has_index = index;
+	struct merge_options o;
+	struct object_id c_tree;
+	struct object_id index_tree;
+	struct commit *result;
+	const struct object_id *bases[1];
+
+	read_cache_preload(NULL);
+	if (refresh_cache(REFRESH_QUIET))
+		return -1;
+
+	if (write_cache_as_tree(&c_tree, 0, NULL) || reset_tree(&c_tree, 0, 0))
+		return error(_("cannot apply a stash in the middle of a merge"));
+
+	if (index) {
+		if (!oidcmp(&info->b_tree, &info->i_tree) ||
+		    !oidcmp(&c_tree, &info->i_tree)) {
+			has_index = 0;
+		} else {
+			struct strbuf out = STRBUF_INIT;
+
+			if (diff_tree_binary(&out, &info->w_commit)) {
+				strbuf_release(&out);
+				return -1;
+			}
+
+			ret = apply_cached(&out);
+			strbuf_release(&out);
+			if (ret)
+				return -1;
+
+			discard_cache();
+			read_cache();
+			if (write_cache_as_tree(&index_tree, 0, NULL))
+				return -1;
+
+			reset_head();
+		}
+	}
+
+	if (info->has_u && restore_untracked(&info->u_tree))
+		return error(_("could not restore untracked files from stash"));
+
+	init_merge_options(&o);
+
+	o.branch1 = "Updated upstream";
+	o.branch2 = "Stashed changes";
+
+	if (!oidcmp(&info->b_tree, &c_tree))
+		o.branch1 = "Version stash was based on";
+
+	if (quiet)
+		o.verbosity = 0;
+
+	if (o.verbosity >= 3)
+		printf_ln(_("Merging %s with %s"), o.branch1, o.branch2);
+
+	bases[0] = &info->b_tree;
+
+	ret = merge_recursive_generic(&o, &c_tree, &info->w_tree, 1, bases,
+				      &result);
+	if (ret) {
+		rerere(0);
+
+		if (index)
+			fprintf_ln(stderr, _("Index was not unstashed."));
+
+		return ret;
+	}
+
+	if (has_index) {
+		if (reset_tree(&index_tree, 0, 0))
+			return -1;
+	} else {
+		struct strbuf out = STRBUF_INIT;
+
+		if (get_newly_staged(&out, &c_tree)) {
+			strbuf_release(&out);
+			return -1;
+		}
+
+		if (reset_tree(&c_tree, 0, 1)) {
+			strbuf_release(&out);
+			return -1;
+		}
+
+		ret = update_index(&out);
+		strbuf_release(&out);
+		if (ret)
+			return -1;
+
+		discard_cache();
+	}
+
+	if (quiet) {
+		if (refresh_cache(REFRESH_QUIET))
+			warning("could not refresh index");
+	} else {
+		struct child_process cp = CHILD_PROCESS_INIT;
+
+		/*
+		 * Status is quite simple and could be replaced with calls to
+		 * wt_status in the future, but it adds complexities which may
+		 * require more tests.
+		 */
+		cp.git_cmd = 1;
+		cp.dir = prefix;
+		argv_array_push(&cp.args, "status");
+		run_command(&cp);
+	}
+
+	return 0;
+}
+
+static int apply_stash(int argc, const char **argv, const char *prefix)
+{
+	int ret;
+	int quiet = 0;
+	int index = 0;
+	struct stash_info info;
+	struct option options[] = {
+		OPT__QUIET(&quiet, N_("be quiet, only report errors")),
+		OPT_BOOL(0, "index", &index,
+			 N_("attempt to recreate the index")),
+		OPT_END()
+	};
+
+	argc = parse_options(argc, argv, prefix, options,
+			     git_stash_helper_apply_usage, 0);
+
+	if (get_stash_info(&info, argc, argv))
+		return -1;
+
+	ret = do_apply_stash(prefix, &info, index, quiet);
+	free_stash_info(&info);
+	return ret;
+}
+
+int cmd_stash__helper(int argc, const char **argv, const char *prefix)
+{
+	pid_t pid = getpid();
+	const char *index_file;
+
+	struct option options[] = {
+		OPT_END()
+	};
+
+	git_config(git_default_config, NULL);
+
+	argc = parse_options(argc, argv, prefix, options, git_stash_helper_usage,
+			     PARSE_OPT_KEEP_UNKNOWN | PARSE_OPT_KEEP_DASHDASH);
+
+	index_file = get_index_file();
+	strbuf_addf(&stash_index_path, "%s.stash.%" PRIuMAX, index_file,
+		    (uintmax_t)pid);
+
+	if (argc < 1)
+		usage_with_options(git_stash_helper_usage, options);
+	if (!strcmp(argv[0], "apply"))
+		return !!apply_stash(argc, argv, prefix);
+
+	usage_msg_opt(xstrfmt(_("unknown subcommand: %s"), argv[0]),
+		      git_stash_helper_usage, options);
+}
diff --git a/git-stash.sh b/git-stash.sh
index 94793c1a91..809b1c2d1d 100755
--- a/git-stash.sh
+++ b/git-stash.sh
@@ -566,76 +566,11 @@ assert_stash_ref() {
 }
 
 apply_stash () {
-
-	assert_stash_like "$@"
-
-	git update-index -q --refresh || die "$(gettext "unable to refresh index")"
-
-	# current index state
-	c_tree=$(git write-tree) ||
-		die "$(gettext "Cannot apply a stash in the middle of a merge")"
-
-	unstashed_index_tree=
-	if test -n "$INDEX_OPTION" && test "$b_tree" != "$i_tree" &&
-			test "$c_tree" != "$i_tree"
-	then
-		git diff-tree --binary $s^2^..$s^2 | git apply --cached
-		test $? -ne 0 &&
-			die "$(gettext "Conflicts in index. Try without --index.")"
-		unstashed_index_tree=$(git write-tree) ||
-			die "$(gettext "Could not save index tree")"
-		git reset
-	fi
-
-	if test -n "$u_tree"
-	then
-		GIT_INDEX_FILE="$TMPindex" git read-tree "$u_tree" &&
-		GIT_INDEX_FILE="$TMPindex" git checkout-index --all &&
-		rm -f "$TMPindex" ||
-		die "$(gettext "Could not restore untracked files from stash entry")"
-	fi
-
-	eval "
-		GITHEAD_$w_tree='Stashed changes' &&
-		GITHEAD_$c_tree='Updated upstream' &&
-		GITHEAD_$b_tree='Version stash was based on' &&
-		export GITHEAD_$w_tree GITHEAD_$c_tree GITHEAD_$b_tree
-	"
-
-	if test -n "$GIT_QUIET"
-	then
-		GIT_MERGE_VERBOSITY=0 && export GIT_MERGE_VERBOSITY
-	fi
-	if git merge-recursive $b_tree -- $c_tree $w_tree
-	then
-		# No conflict
-		if test -n "$unstashed_index_tree"
-		then
-			git read-tree "$unstashed_index_tree"
-		else
-			a="$TMP-added" &&
-			git diff-index --cached --name-only --diff-filter=A $c_tree >"$a" &&
-			git read-tree --reset $c_tree &&
-			git update-index --add --stdin <"$a" ||
-				die "$(gettext "Cannot unstage modified files")"
-			rm -f "$a"
-		fi
-		squelch=
-		if test -n "$GIT_QUIET"
-		then
-			squelch='>/dev/null 2>&1'
-		fi
-		(cd "$START_DIR" && eval "git status $squelch") || :
-	else
-		# Merge conflict; keep the exit status from merge-recursive
-		status=$?
-		git rerere
-		if test -n "$INDEX_OPTION"
-		then
-			gettextln "Index was not unstashed." >&2
-		fi
-		exit $status
-	fi
+	cd "$START_DIR"
+	git stash--helper apply "$@"
+	res=$?
+	cd_to_toplevel
+	return $res
 }
 
 pop_stash() {
@@ -713,7 +648,8 @@ push)
 	;;
 apply)
 	shift
-	apply_stash "$@"
+	cd "$START_DIR"
+	git stash--helper apply "$@"
 	;;
 clear)
 	shift
diff --git a/git.c b/git.c
index c27c38738b..3c0e762d7d 100644
--- a/git.c
+++ b/git.c
@@ -544,6 +544,7 @@ static struct cmd_struct commands[] = {
 	{ "show-index", cmd_show_index },
 	{ "show-ref", cmd_show_ref, RUN_SETUP },
 	{ "stage", cmd_add, RUN_SETUP | NEED_WORK_TREE },
+	{ "stash--helper", cmd_stash__helper, RUN_SETUP | NEED_WORK_TREE },
 	{ "status", cmd_status, RUN_SETUP | NEED_WORK_TREE },
 	{ "stripspace", cmd_stripspace },
 	{ "submodule--helper", cmd_submodule__helper, RUN_SETUP | SUPPORT_SUPER_PREFIX | NO_PARSEOPT },
