diff --git a/builtin-apply.c b/builtin-apply.c
index 1beebe5ff1..12f00e38db 100644
--- a/builtin-apply.c
+++ b/builtin-apply.c
@@ -144,6 +144,7 @@ struct patch {
 	unsigned long deflate_origlen;
 	int lines_added, lines_deleted;
 	int score;
+	unsigned int is_toplevel_relative:1;
 	unsigned int inaccurate_eof:1;
 	unsigned int is_binary:1;
 	unsigned int is_copy:1;
@@ -362,7 +363,7 @@ static int gitdiff_hdrend(const char *line, struct patch *patch)
 static char *gitdiff_verify_name(const char *line, int isnull, char *orig_name, const char *oldnew)
 {
 	if (!orig_name && !isnull)
-		return find_name(line, NULL, p_value, TERM_TAB);
+		return find_name(line, NULL, 1, TERM_TAB);
 
 	if (orig_name) {
 		int len;
@@ -372,7 +373,7 @@ static char *gitdiff_verify_name(const char *line, int isnull, char *orig_name,
 		len = strlen(name);
 		if (isnull)
 			die("git-apply: bad git-diff - expected /dev/null, got %s on line %d", name, linenr);
-		another = find_name(line, NULL, p_value, TERM_TAB);
+		another = find_name(line, NULL, 1, TERM_TAB);
 		if (!another || memcmp(another, name, len))
 			die("git-apply: bad git-diff - inconsistent %s filename on line %d", oldnew, linenr);
 		free(another);
@@ -427,28 +428,28 @@ static int gitdiff_newfile(const char *line, struct patch *patch)
 static int gitdiff_copysrc(const char *line, struct patch *patch)
 {
 	patch->is_copy = 1;
-	patch->old_name = find_name(line, NULL, p_value-1, 0);
+	patch->old_name = find_name(line, NULL, 0, 0);
 	return 0;
 }
 
 static int gitdiff_copydst(const char *line, struct patch *patch)
 {
 	patch->is_copy = 1;
-	patch->new_name = find_name(line, NULL, p_value-1, 0);
+	patch->new_name = find_name(line, NULL, 0, 0);
 	return 0;
 }
 
 static int gitdiff_renamesrc(const char *line, struct patch *patch)
 {
 	patch->is_rename = 1;
-	patch->old_name = find_name(line, NULL, p_value-1, 0);
+	patch->old_name = find_name(line, NULL, 0, 0);
 	return 0;
 }
 
 static int gitdiff_renamedst(const char *line, struct patch *patch)
 {
 	patch->is_rename = 1;
-	patch->new_name = find_name(line, NULL, p_value-1, 0);
+	patch->new_name = find_name(line, NULL, 0, 0);
 	return 0;
 }
 
@@ -787,6 +788,7 @@ static int find_header(char *line, unsigned long size, int *hdrsize, struct patc
 {
 	unsigned long offset, len;
 
+	patch->is_toplevel_relative = 0;
 	patch->is_rename = patch->is_copy = 0;
 	patch->is_new = patch->is_delete = -1;
 	patch->old_mode = patch->new_mode = 0;
@@ -831,6 +833,7 @@ static int find_header(char *line, unsigned long size, int *hdrsize, struct patc
 					die("git diff header lacks filename information (line %d)", linenr);
 				patch->old_name = patch->new_name = patch->def_name;
 			}
+			patch->is_toplevel_relative = 1;
 			*hdrsize = git_hdr_len;
 			return offset;
 		}
@@ -2499,6 +2502,12 @@ static int use_patch(struct patch *p)
 			return 0;
 		x = x->next;
 	}
+	if (0 < prefix_length) {
+		int pathlen = strlen(pathname);
+		if (pathlen <= prefix_length ||
+		    memcmp(prefix, pathname, prefix_length))
+			return 0;
+	}
 	return 1;
 }
 
@@ -2513,7 +2522,7 @@ static void prefix_one(char **name)
 
 static void prefix_patches(struct patch *p)
 {
-	if (!prefix)
+	if (!prefix || p->is_toplevel_relative)
 		return;
 	for ( ; p; p = p->next) {
 		if (p->new_name == p->old_name) {
diff --git a/t/t4119-apply-config.sh b/t/t4119-apply-config.sh
index f9b9425153..32e0d7172e 100755
--- a/t/t4119-apply-config.sh
+++ b/t/t4119-apply-config.sh
@@ -78,7 +78,7 @@ test_expect_success 'apply --whitespace=strip in subdir' '
 	git update-index --refresh &&
 
 	cd sub &&
-	git apply --whitespace=strip -p2 ../patch.file &&
+	git apply --whitespace=strip ../patch.file &&
 	if grep " " file1
 	then
 		echo "Eh?"
@@ -101,7 +101,7 @@ test_expect_success 'apply --whitespace=strip from config in subdir' '
 	git update-index --refresh &&
 
 	cd sub &&
-	git apply -p2 ../patch.file &&
+	git apply ../patch.file &&
 	if grep " " file1
 	then
 		echo "Eh?"