diff --git a/apply.c b/apply.c
index 821fe411ec..5eec433583 100644
--- a/apply.c
+++ b/apply.c
@@ -4105,7 +4105,7 @@ static int preimage_oid_in_gitlink_patch(struct patch *p, struct object_id *oid)
 static int build_fake_ancestor(struct apply_state *state, struct patch *list)
 {
 	struct patch *patch;
-	struct index_state result = INDEX_STATE_INIT;
+	struct index_state result = INDEX_STATE_INIT(state->repo);
 	struct lock_file lock = LOCK_INIT;
 	int res;
 
diff --git a/builtin/difftool.c b/builtin/difftool.c
index 758e7bd3b6..dbbfb19f19 100644
--- a/builtin/difftool.c
+++ b/builtin/difftool.c
@@ -361,7 +361,7 @@ static int run_dir_diff(const char *extcmd, int symlinks, const char *prefix,
 	struct hashmap symlinks2 = HASHMAP_INIT(pair_cmp, NULL);
 	struct hashmap_iter iter;
 	struct pair_entry *entry;
-	struct index_state wtindex = INDEX_STATE_INIT;
+	struct index_state wtindex = INDEX_STATE_INIT(the_repository);
 	struct checkout lstate, rstate;
 	int err = 0;
 	struct child_process cmd = CHILD_PROCESS_INIT;
diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index dc332c6d05..c373815491 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -217,7 +217,7 @@ static int update_working_directory(struct pattern_list *pl)
 	o.head_idx = -1;
 	o.src_index = r->index;
 	o.dst_index = r->index;
-	index_state_init(&o.result);
+	index_state_init(&o.result, r);
 	o.skip_sparse_checkout = 0;
 	o.pl = pl;
 
diff --git a/builtin/stash.c b/builtin/stash.c
index a5f13fb1e9..839569a980 100644
--- a/builtin/stash.c
+++ b/builtin/stash.c
@@ -1137,7 +1137,7 @@ static int save_untracked_files(struct stash_info *info, struct strbuf *msg,
 	int ret = 0;
 	struct strbuf untracked_msg = STRBUF_INIT;
 	struct child_process cp_upd_index = CHILD_PROCESS_INIT;
-	struct index_state istate = INDEX_STATE_INIT;
+	struct index_state istate = INDEX_STATE_INIT(the_repository);
 
 	cp_upd_index.git_cmd = 1;
 	strvec_pushl(&cp_upd_index.args, "update-index", "-z", "--add",
@@ -1176,7 +1176,7 @@ static int stash_staged(struct stash_info *info, struct strbuf *out_patch,
 {
 	int ret = 0;
 	struct child_process cp_diff_tree = CHILD_PROCESS_INIT;
-	struct index_state istate = INDEX_STATE_INIT;
+	struct index_state istate = INDEX_STATE_INIT(the_repository);
 
 	if (write_index_as_tree(&info->w_tree, &istate, the_repository->index_file,
 				0, NULL)) {
@@ -1209,7 +1209,7 @@ static int stash_patch(struct stash_info *info, const struct pathspec *ps,
 	int ret = 0;
 	struct child_process cp_read_tree = CHILD_PROCESS_INIT;
 	struct child_process cp_diff_tree = CHILD_PROCESS_INIT;
-	struct index_state istate = INDEX_STATE_INIT;
+	struct index_state istate = INDEX_STATE_INIT(the_repository);
 	char *old_index_env = NULL, *old_repo_index_file;
 
 	remove_path(stash_index_path.buf);
@@ -1271,7 +1271,7 @@ static int stash_working_tree(struct stash_info *info, const struct pathspec *ps
 	struct rev_info rev;
 	struct child_process cp_upd_index = CHILD_PROCESS_INIT;
 	struct strbuf diff_output = STRBUF_INIT;
-	struct index_state istate = INDEX_STATE_INIT;
+	struct index_state istate = INDEX_STATE_INIT(the_repository);
 
 	init_revisions(&rev, NULL);
 	copy_pathspec(&rev.prune_data, ps);
diff --git a/builtin/worktree.c b/builtin/worktree.c
index 311d6e9075..f51c40f1e1 100644
--- a/builtin/worktree.c
+++ b/builtin/worktree.c
@@ -923,7 +923,7 @@ static int unlock_worktree(int ac, const char **av, const char *prefix)
 
 static void validate_no_submodules(const struct worktree *wt)
 {
-	struct index_state istate = INDEX_STATE_INIT;
+	struct index_state istate = INDEX_STATE_INIT(the_repository);
 	struct strbuf path = STRBUF_INIT;
 	int i, found_submodules = 0;
 
diff --git a/cache.h b/cache.h
index be28fce12a..4bf14e0bd9 100644
--- a/cache.h
+++ b/cache.h
@@ -367,10 +367,13 @@ struct index_state {
  * If the variable won't be used again, use release_index() to free()
  * its resources. If it needs to be used again use discard_index(),
  * which does the same thing, but will use use index_state_init() at
- * the end.
+ * the end. The discard_index() will use its own "istate->repo" as the
+ * "r" argument to index_state_init() in that case.
  */
-#define INDEX_STATE_INIT { 0 }
-void index_state_init(struct index_state *istate);
+#define INDEX_STATE_INIT(r) { \
+	.repo = (r), \
+}
+void index_state_init(struct index_state *istate, struct repository *r);
 void release_index(struct index_state *istate);
 
 /* Name hashing */
diff --git a/fsmonitor-settings.c b/fsmonitor-settings.c
index ee63a97dc5..899bfe9c81 100644
--- a/fsmonitor-settings.c
+++ b/fsmonitor-settings.c
@@ -143,8 +143,6 @@ static void lookup_fsmonitor_settings(struct repository *r)
 
 enum fsmonitor_mode fsm_settings__get_mode(struct repository *r)
 {
-	if (!r)
-		r = the_repository;
 	if (!r->settings.fsmonitor)
 		lookup_fsmonitor_settings(r);
 
@@ -153,8 +151,6 @@ enum fsmonitor_mode fsm_settings__get_mode(struct repository *r)
 
 const char *fsm_settings__get_hook_path(struct repository *r)
 {
-	if (!r)
-		r = the_repository;
 	if (!r->settings.fsmonitor)
 		lookup_fsmonitor_settings(r);
 
@@ -174,8 +170,6 @@ void fsm_settings__set_ipc(struct repository *r)
 	 * Caller requested IPC explicitly, so avoid (possibly
 	 * recursive) config lookup.
 	 */
-	if (!r)
-		r = the_repository;
 	if (!r->settings.fsmonitor)
 		r->settings.fsmonitor = alloc_settings();
 
@@ -197,8 +191,6 @@ void fsm_settings__set_hook(struct repository *r, const char *path)
 	 * Caller requested hook explicitly, so avoid (possibly
 	 * recursive) config lookup.
 	 */
-	if (!r)
-		r = the_repository;
 	if (!r->settings.fsmonitor)
 		r->settings.fsmonitor = alloc_settings();
 
@@ -210,8 +202,6 @@ void fsm_settings__set_hook(struct repository *r, const char *path)
 
 void fsm_settings__set_disabled(struct repository *r)
 {
-	if (!r)
-		r = the_repository;
 	if (!r->settings.fsmonitor)
 		r->settings.fsmonitor = alloc_settings();
 
@@ -223,8 +213,6 @@ void fsm_settings__set_disabled(struct repository *r)
 void fsm_settings__set_incompatible(struct repository *r,
 				    enum fsmonitor_reason reason)
 {
-	if (!r)
-		r = the_repository;
 	if (!r->settings.fsmonitor)
 		r->settings.fsmonitor = alloc_settings();
 
@@ -235,8 +223,6 @@ void fsm_settings__set_incompatible(struct repository *r,
 
 enum fsmonitor_reason fsm_settings__get_reason(struct repository *r)
 {
-	if (!r)
-		r = the_repository;
 	if (!r->settings.fsmonitor)
 		lookup_fsmonitor_settings(r);
 
diff --git a/fsmonitor.c b/fsmonitor.c
index 08af00c738..a5b9e75437 100644
--- a/fsmonitor.c
+++ b/fsmonitor.c
@@ -304,7 +304,7 @@ void refresh_fsmonitor(struct index_state *istate)
 	char *buf;
 	unsigned int i;
 	int is_trivial = 0;
-	struct repository *r = istate->repo ? istate->repo : the_repository;
+	struct repository *r = istate->repo;
 	enum fsmonitor_mode fsm_mode = fsm_settings__get_mode(r);
 	enum fsmonitor_reason reason = fsm_settings__get_reason(r);
 
diff --git a/merge-recursive.c b/merge-recursive.c
index 0948b3ea96..ae469f8cc8 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -412,7 +412,7 @@ static int unpack_trees_start(struct merge_options *opt,
 {
 	int rc;
 	struct tree_desc t[3];
-	struct index_state tmp_index = INDEX_STATE_INIT;
+	struct index_state tmp_index = INDEX_STATE_INIT(opt->repo);
 
 	memset(&opt->priv->unpack_opts, 0, sizeof(opt->priv->unpack_opts));
 	if (opt->priv->call_depth)
diff --git a/read-cache.c b/read-cache.c
index d191741f60..7bd12afb38 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -2300,8 +2300,6 @@ static void set_new_index_sparsity(struct index_state *istate)
 	 * If the index's repo exists, mark it sparse according to
 	 * repo settings.
 	 */
-	if (!istate->repo)
-		return;
 	prepare_repo_settings(istate->repo);
 	if (!istate->repo->settings.command_requires_full_index &&
 	    is_sparse_index_allowed(istate, 0))
@@ -2330,8 +2328,6 @@ int do_read_index(struct index_state *istate, const char *path, int must_exist)
 	fd = open(path, O_RDONLY);
 	if (fd < 0) {
 		if (!must_exist && errno == ENOENT) {
-			if (!istate->repo)
-				istate->repo = the_repository;
 			set_new_index_sparsity(istate);
 			return 0;
 		}
@@ -2433,9 +2429,6 @@ int do_read_index(struct index_state *istate, const char *path, int must_exist)
 	trace2_data_intmax("index", the_repository, "read/cache_nr",
 			   istate->cache_nr);
 
-	if (!istate->repo)
-		istate->repo = the_repository;
-
 	/*
 	 * If the command explicitly requires a full index, force it
 	 * to be full. Otherwise, correct the sparsity based on repository
@@ -2501,7 +2494,7 @@ int read_index_from(struct index_state *istate, const char *path,
 		release_index(split_index->base);
 	else
 		ALLOC_ARRAY(split_index->base, 1);
-	index_state_init(split_index->base);
+	index_state_init(split_index->base, istate->repo);
 
 	base_oid_hex = oid_to_hex(&split_index->base_oid);
 	base_path = xstrfmt("%s/sharedindex.%s", gitdir, base_oid_hex);
@@ -2540,9 +2533,9 @@ int is_index_unborn(struct index_state *istate)
 	return (!istate->cache_nr && !istate->timestamp.sec);
 }
 
-void index_state_init(struct index_state *istate)
+void index_state_init(struct index_state *istate, struct repository *r)
 {
-	struct index_state blank = INDEX_STATE_INIT;
+	struct index_state blank = INDEX_STATE_INIT(r);
 	memcpy(istate, &blank, sizeof(*istate));
 }
 
@@ -2579,7 +2572,7 @@ void release_index(struct index_state *istate)
 void discard_index(struct index_state *istate)
 {
 	release_index(istate);
-	index_state_init(istate);
+	index_state_init(istate, istate->repo);
 }
 
 /*
@@ -2933,7 +2926,7 @@ static int do_write_index(struct index_state *istate, struct tempfile *tempfile,
 	int ieot_entries = 1;
 	struct index_entry_offset_table *ieot = NULL;
 	int nr, nr_threads;
-	struct repository *r = istate->repo ? istate->repo : the_repository;
+	struct repository *r = istate->repo;
 
 	f = hashfd(tempfile->fd, tempfile->filename.buf);
 
diff --git a/repository.c b/repository.c
index a5805fa33b..937fa974b3 100644
--- a/repository.c
+++ b/repository.c
@@ -28,6 +28,8 @@ void initialize_the_repository(void)
 	the_repo.remote_state = remote_state_new();
 	the_repo.parsed_objects = parsed_object_pool_new();
 
+	index_state_init(&the_index, the_repository);
+
 	repo_set_hash_algo(&the_repo, GIT_HASH_SHA1);
 }
 
@@ -302,16 +304,13 @@ int repo_read_index(struct repository *repo)
 {
 	int res;
 
+	/* Complete the double-reference */
 	if (!repo->index) {
 		ALLOC_ARRAY(repo->index, 1);
-		index_state_init(repo->index);
-	}
-
-	/* Complete the double-reference */
-	if (!repo->index->repo)
-		repo->index->repo = repo;
-	else if (repo->index->repo != repo)
+		index_state_init(repo->index, repo);
+	} else if (repo->index->repo != repo) {
 		BUG("repo's index should point back at itself");
+	}
 
 	res = read_index_from(repo->index, repo->index_file, repo->gitdir);
 
diff --git a/revision.c b/revision.c
index fb090886f5..21f5f572c2 100644
--- a/revision.c
+++ b/revision.c
@@ -1813,7 +1813,7 @@ void add_index_objects_to_pending(struct rev_info *revs, unsigned int flags)
 	worktrees = get_worktrees();
 	for (p = worktrees; *p; p++) {
 		struct worktree *wt = *p;
-		struct index_state istate = INDEX_STATE_INIT;
+		struct index_state istate = INDEX_STATE_INIT(revs->repo);
 
 		if (wt->is_current)
 			continue; /* current index already taken care of */
diff --git a/sparse-index.c b/sparse-index.c
index 86e3b99870..147a13386a 100644
--- a/sparse-index.c
+++ b/sparse-index.c
@@ -128,9 +128,6 @@ int is_sparse_index_allowed(struct index_state *istate, int flags)
 	if (!core_apply_sparse_checkout || !core_sparse_checkout_cone)
 		return 0;
 
-	if (!istate->repo)
-		istate->repo = the_repository;
-
 	if (!(flags & SPARSE_INDEX_MEMORY_ONLY)) {
 		int test_env;
 
@@ -327,9 +324,6 @@ void expand_index(struct index_state *istate, struct pattern_list *pl)
 			pl = NULL;
 	}
 
-	if (!istate->repo)
-		istate->repo = the_repository;
-
 	/*
 	 * A NULL pattern set indicates we are expanding a full index, so
 	 * we use a special region name that indicates the full expansion.
@@ -552,9 +546,6 @@ void expand_to_path(struct index_state *istate,
 	if (!istate->sparse_index)
 		return;
 
-	if (!istate->repo)
-		istate->repo = the_repository;
-
 	in_expand_to_path = 1;
 
 	/*
diff --git a/split-index.c b/split-index.c
index a5b56c0c37..5d0f04763e 100644
--- a/split-index.c
+++ b/split-index.c
@@ -91,7 +91,7 @@ void move_cache_to_base_index(struct index_state *istate)
 	}
 
 	ALLOC_ARRAY(si->base, 1);
-	index_state_init(si->base);
+	index_state_init(si->base, istate->repo);
 	si->base->version = istate->version;
 	/* zero timestamp disables racy test in ce_write_index() */
 	si->base->timestamp = istate->timestamp;
diff --git a/unpack-trees.c b/unpack-trees.c
index d1d1b0f319..3d05e45a27 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -1905,7 +1905,7 @@ int unpack_trees(unsigned len, struct tree_desc *t, struct unpack_trees_options
 		populate_from_existing_patterns(o, &pl);
 	}
 
-	index_state_init(&o->result);
+	index_state_init(&o->result, o->src_index->repo);
 	o->result.initialized = 1;
 	o->result.timestamp.sec = o->src_index->timestamp.sec;
 	o->result.timestamp.nsec = o->src_index->timestamp.nsec;