diff --git a/combine-diff.c b/combine-diff.c
index 3878faabe7bb2f..305414efdf436d 100644
--- a/combine-diff.c
+++ b/combine-diff.c
@@ -1515,7 +1515,6 @@ void diff_tree_combined(const struct object_id *oid,
 
 	diffopts = *opt;
 	copy_pathspec(&diffopts.pathspec, &opt->pathspec);
-	diffopts.flags.recursive = 1;
 	diffopts.flags.allow_external = 0;
 
 	/* find set of paths that everybody touches
diff --git a/submodule.c b/submodule.c
index fff3c755703163..1c273ec87fa865 100644
--- a/submodule.c
+++ b/submodule.c
@@ -916,6 +916,7 @@ static void collect_changed_submodules(struct repository *r,
 		diff_rev.diffopt.output_format |= DIFF_FORMAT_CALLBACK;
 		diff_rev.diffopt.format_callback = collect_changed_submodules_cb;
 		diff_rev.diffopt.format_callback_data = &data;
+		diff_rev.diffopt.flags.recursive = 1;
 		diff_rev.dense_combined_merges = 1;
 		diff_tree_combined_merge(commit, &diff_rev);
 		release_revisions(&diff_rev);
diff --git a/t/t4013/diff.diff-tree_-c_--abbrev_master b/t/t4013/diff.diff-tree_-c_--abbrev_master
index b8e4aa2530717a..1f00877ca5ee51 100644
--- a/t/t4013/diff.diff-tree_-c_--abbrev_master
+++ b/t/t4013/diff.diff-tree_-c_--abbrev_master
@@ -1,5 +1,5 @@
 $ git diff-tree -c --abbrev master
 59d314ad6f356dd08601a4cd5e530381da3e3c64
-::100644 100644 100644 cead32e... 7289e35... 992913c... MM	dir/sub
+::040000 040000 040000 65f5c9d... f977ed4... 0564e02... MM	dir
 ::100644 100644 100644 b414108... f4615da... 10a8a9f... MM	file0
 $
diff --git a/t/t4013/diff.diff-tree_-c_-r_master b/t/t4013/diff.diff-tree_-c_-r_master
new file mode 100644
index 00000000000000..8980be87440791
--- /dev/null
+++ b/t/t4013/diff.diff-tree_-c_-r_master
@@ -0,0 +1,5 @@
+$ git diff-tree -c -r master
+59d314ad6f356dd08601a4cd5e530381da3e3c64
+::100644 100644 100644 cead32e925b1420c84c14cbf7cf755e7e45af8ad 7289e35bff32727c08dda207511bec138fdb9ea5 992913c5aa0a5476d10c49ed0f21fc0c6d1aedf3 MM	dir/sub
+::100644 100644 100644 b414108e81e5091fe0974a1858b4d0d22b107f70 f4615da674c09df322d6ba8d6b21ecfb1b1ba510 10a8a9f3657f91a156b9f0184ed79a20adef9f7f MM	file0
+$
diff --git a/t/t4013/diff.diff-tree_-c_master b/t/t4013/diff.diff-tree_-c_master
index e2d2bb26114ac8..1ecc2cfc6c50e9 100644
--- a/t/t4013/diff.diff-tree_-c_master
+++ b/t/t4013/diff.diff-tree_-c_master
@@ -1,5 +1,5 @@
 $ git diff-tree -c master
 59d314ad6f356dd08601a4cd5e530381da3e3c64
-::100644 100644 100644 cead32e925b1420c84c14cbf7cf755e7e45af8ad 7289e35bff32727c08dda207511bec138fdb9ea5 992913c5aa0a5476d10c49ed0f21fc0c6d1aedf3 MM	dir/sub
+::040000 040000 040000 65f5c9dd60ce3b2b3324b618ac7accf8d912c113 f977ed46ae6873c1c30ab878e15a4accedc3618b 0564e026437809817a64fff393079714b6dd4628 MM	dir
 ::100644 100644 100644 b414108e81e5091fe0974a1858b4d0d22b107f70 f4615da674c09df322d6ba8d6b21ecfb1b1ba510 10a8a9f3657f91a156b9f0184ed79a20adef9f7f MM	file0
 $
diff --git a/t/t4013/diff.noellipses-diff-tree_-c_--abbrev_master b/t/t4013/diff.noellipses-diff-tree_-c_--abbrev_master
index bb80f013b37da0..62d655dac240a8 100644
--- a/t/t4013/diff.noellipses-diff-tree_-c_--abbrev_master
+++ b/t/t4013/diff.noellipses-diff-tree_-c_--abbrev_master
@@ -1,5 +1,5 @@
 $ git diff-tree -c --abbrev master
 59d314ad6f356dd08601a4cd5e530381da3e3c64
-::100644 100644 100644 cead32e 7289e35 992913c MM	dir/sub
+::040000 040000 040000 65f5c9d f977ed4 0564e02 MM	dir
 ::100644 100644 100644 b414108 f4615da 10a8a9f MM	file0
 $
diff --git a/t/t8020-last-modified.sh b/t/t8020-last-modified.sh
index 5eb4cef0359212..ff837a40f40b8c 100755
--- a/t/t8020-last-modified.sh
+++ b/t/t8020-last-modified.sh
@@ -128,6 +128,22 @@ test_expect_success 'only last-modified files in the current tree' '
 	EOF
 '
 
+test_expect_success 'last-modified with files in a subdir merged' '
+	git checkout -b branch-k1 1 &&
+	mkdir a k &&
+	test_commit k1 a/file2 &&
+	git checkout -b branch-k2 &&
+	test_commit k2 k/file2 &&
+	git checkout branch-k1 &&
+	test_merge km2 branch-k2 &&
+	test_merge km3 3 &&
+	check_last_modified <<-\EOF
+	km3 a
+	k2 k
+	1 file
+	EOF
+'
+
 test_expect_success 'cross merge boundaries in blaming' '
 	git checkout HEAD^0 &&
 	git rm -rf . &&