diff --git a/t/t1400-update-ref.sh b/t/t1400-update-ref.sh
index 4d66cd7f4a1..91cc6dff724 100755
--- a/t/t1400-update-ref.sh
+++ b/t/t1400-update-ref.sh
@@ -9,8 +9,6 @@ test_description='Test git update-ref and basic ref logging'
 Z=$ZERO_OID
 
 m=refs/heads/main
-n_dir=refs/heads/gu
-n=$n_dir/fixes
 outside=refs/foo
 bare=bare-repo
 
@@ -62,10 +60,10 @@ test_expect_success "delete $m without oldvalue verification" '
 	test_must_fail git show-ref --verify -q $m
 '
 
-test_expect_success "fail to create $n" '
-	test_when_finished "rm -f .git/$n_dir" &&
-	touch .git/$n_dir &&
-	test_must_fail git update-ref $n $A
+test_expect_success "fail to create $n due to file/directory conflict" '
+	test_when_finished "git update-ref -d refs/heads/gu" &&
+	git update-ref refs/heads/gu $A &&
+	test_must_fail git update-ref refs/heads/gu/fixes $A
 '
 
 test_expect_success "create $m (by HEAD)" '
@@ -221,16 +219,16 @@ test_expect_success 'delete symref without dereference when the referred ref is
 '
 
 test_expect_success 'update-ref -d is not confused by self-reference' '
+	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF refs/heads/self" &&
 	git symbolic-ref refs/heads/self refs/heads/self &&
-	test_when_finished "rm -f .git/refs/heads/self" &&
 	test_path_is_file .git/refs/heads/self &&
 	test_must_fail git update-ref -d refs/heads/self &&
 	test_path_is_file .git/refs/heads/self
 '
 
 test_expect_success 'update-ref --no-deref -d can delete self-reference' '
+	test_when_finished "test-tool ref-store main delete-refs REF_NO_DEREF refs/heads/self" &&
 	git symbolic-ref refs/heads/self refs/heads/self &&
-	test_when_finished "rm -f .git/refs/heads/self" &&
 	test_path_is_file .git/refs/heads/self &&
 	git update-ref --no-deref -d refs/heads/self &&
 	test_must_fail git show-ref --verify -q refs/heads/self
@@ -434,7 +432,8 @@ test_expect_success 'Query "main@{2005-05-28}" (past end of history)' '
 	test_i18ngrep -F "warning: log for ref $m unexpectedly ended on $ld" e
 '
 
-rm -f .git/$m .git/logs/$m expect
+rm -f expect
+git update-ref -d $m
 
 test_expect_success 'creating initial files' '
 	test_when_finished rm -f M &&
diff --git a/t/t1450-fsck.sh b/t/t1450-fsck.sh
index 10a539158c4..f55b539b083 100755
--- a/t/t1450-fsck.sh
+++ b/t/t1450-fsck.sh
@@ -15,6 +15,7 @@ test_expect_success setup '
 	git config --unset i18n.commitencoding &&
 	git checkout HEAD^0 &&
 	test_commit B fileB two &&
+	orig_head=$(git rev-parse HEAD) &&
 	git tag -d A B &&
 	git reflog expire --expire=now --all
 '
@@ -115,15 +116,15 @@ test_expect_success 'zlib corrupt loose object output ' '
 '
 
 test_expect_success 'branch pointing to non-commit' '
-	git rev-parse HEAD^{tree} >.git/refs/heads/invalid &&
+	tree_oid=$(git rev-parse --verify HEAD^{tree}) &&
 	test_when_finished "git update-ref -d refs/heads/invalid" &&
+	test-tool ref-store main update-ref msg refs/heads/invalid $tree_oid $ZERO_OID REF_SKIP_OID_VERIFICATION &&
 	test_must_fail git fsck 2>out &&
 	test_i18ngrep "not a commit" out
 '
 
 test_expect_success 'HEAD link pointing at a funny object' '
-	test_when_finished "mv .git/SAVED_HEAD .git/HEAD" &&
-	mv .git/HEAD .git/SAVED_HEAD &&
+	test_when_finished "git update-ref HEAD $orig_head" &&
 	echo $ZERO_OID >.git/HEAD &&
 	# avoid corrupt/broken HEAD from interfering with repo discovery
 	test_must_fail env GIT_DIR=.git git fsck 2>out &&
@@ -131,8 +132,7 @@ test_expect_success 'HEAD link pointing at a funny object' '
 '
 
 test_expect_success 'HEAD link pointing at a funny place' '
-	test_when_finished "mv .git/SAVED_HEAD .git/HEAD" &&
-	mv .git/HEAD .git/SAVED_HEAD &&
+	test_when_finished "git update-ref --no-deref HEAD $orig_head" &&
 	echo "ref: refs/funny/place" >.git/HEAD &&
 	# avoid corrupt/broken HEAD from interfering with repo discovery
 	test_must_fail env GIT_DIR=.git git fsck 2>out &&
@@ -140,10 +140,9 @@ test_expect_success 'HEAD link pointing at a funny place' '
 '
 
 test_expect_success 'HEAD link pointing at a funny object (from different wt)' '
-	test_when_finished "mv .git/SAVED_HEAD .git/HEAD" &&
+	test_when_finished "git update-ref HEAD $orig_head" &&
 	test_when_finished "rm -rf .git/worktrees wt" &&
 	git worktree add wt &&
-	mv .git/HEAD .git/SAVED_HEAD &&
 	echo $ZERO_OID >.git/HEAD &&
 	# avoid corrupt/broken HEAD from interfering with repo discovery
 	test_must_fail git -C wt fsck 2>out &&
@@ -161,7 +160,8 @@ test_expect_success 'other worktree HEAD link pointing at a funny object' '
 test_expect_success 'other worktree HEAD link pointing at missing object' '
 	test_when_finished "rm -rf .git/worktrees other" &&
 	git worktree add other &&
-	echo "Contents missing from repo" | git hash-object --stdin >.git/worktrees/other/HEAD &&
+	object_id=$(echo "Contents missing from repo" | git hash-object --stdin) &&
+	test-tool -C other ref-store main update-ref msg HEAD $object_id "" REF_NO_DEREF,REF_SKIP_OID_VERIFICATION &&
 	test_must_fail git fsck 2>out &&
 	test_i18ngrep "worktrees/other/HEAD: invalid sha1 pointer" out
 '
@@ -391,7 +391,7 @@ test_expect_success 'tag pointing to nonexistent' '
 
 	tag=$(git hash-object -t tag -w --stdin <invalid-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/invalid &&
+	git update-ref refs/tags/invalid $tag &&
 	test_when_finished "git update-ref -d refs/tags/invalid" &&
 	test_must_fail git fsck --tags >out &&
 	test_i18ngrep "broken link" out
@@ -411,7 +411,7 @@ test_expect_success 'tag pointing to something else than its type' '
 
 	tag=$(git hash-object -t tag -w --stdin <wrong-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	test_must_fail git fsck --tags
 '
@@ -428,7 +428,7 @@ test_expect_success 'tag with incorrect tag name & missing tagger' '
 
 	tag=$(git hash-object --literally -t tag -w --stdin <wrong-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	git fsck --tags 2>out &&
 
@@ -452,7 +452,7 @@ test_expect_success 'tag with bad tagger' '
 
 	tag=$(git hash-object --literally -t tag -w --stdin <wrong-tag) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	test_must_fail git fsck --tags 2>out &&
 	test_i18ngrep "error in tag .*: invalid author/committer" out
@@ -471,7 +471,7 @@ test_expect_success 'tag with NUL in header' '
 
 	tag=$(git hash-object --literally -t tag -w --stdin <tag-NUL-header) &&
 	test_when_finished "remove_object $tag" &&
-	echo $tag >.git/refs/tags/wrong &&
+	git update-ref refs/tags/wrong $tag &&
 	test_when_finished "git update-ref -d refs/tags/wrong" &&
 	test_must_fail git fsck --tags 2>out &&
 	test_i18ngrep "error in tag $tag.*unterminated header: NUL at offset" out
diff --git a/t/t3404-rebase-interactive.sh b/t/t3404-rebase-interactive.sh
index 8ea2bf13026..d2a7a91f170 100755
--- a/t/t3404-rebase-interactive.sh
+++ b/t/t3404-rebase-interactive.sh
@@ -2160,7 +2160,7 @@ test_expect_success '--update-refs: check failed ref update' '
 	# recorded in the update-refs file. We will force-update the
 	# "second" ref, but "git branch -f" will not work because of
 	# the lock in the update-refs file.
-	git rev-parse third >.git/refs/heads/second &&
+	git update-ref refs/heads/second third &&
 
 	test_must_fail git rebase --continue 2>err &&
 	grep "update_ref failed for ref '\''refs/heads/second'\''" err &&
diff --git a/t/t5526-fetch-submodules.sh b/t/t5526-fetch-submodules.sh
index 26e933f93ae..7ab220fa313 100755
--- a/t/t5526-fetch-submodules.sh
+++ b/t/t5526-fetch-submodules.sh
@@ -771,7 +771,7 @@ test_expect_success 'fetching submodule into a broken repository' '
 	git -C dst fetch --recurse-submodules &&
 
 	# Break the receiving submodule
-	rm -f dst/sub/.git/HEAD &&
+	test-tool -C dst/sub ref-store main delete-refs REF_NO_DEREF msg HEAD &&
 
 	# NOTE: without the fix the following tests will recurse forever!
 	# They should terminate with an error.
