diff --git a/libpkgconf/fragment.c b/libpkgconf/fragment.c
index f41d304..033c2af 100644
--- a/libpkgconf/fragment.c
+++ b/libpkgconf/fragment.c
@@ -38,6 +38,26 @@ pkgconf_fragment_is_unmergeable(const char *string)
 	return false;
 }
 
+static inline bool
+pkgconf_fragment_should_munge(const char *string, const char *sysroot_dir)
+{
+	static struct pkgconf_fragment_check check_fragments[] = {
+		{"-isystem", 8},
+	};
+
+	if (*string != '/')
+		return false;
+
+	if (sysroot_dir != NULL && strncmp(sysroot_dir, string, strlen(sysroot_dir)))
+		return true;
+
+	for (size_t i = 0; i < PKGCONF_ARRAY_SIZE(check_fragments); i++)
+		if (!strncmp(string, check_fragments[i].token, check_fragments[i].len))
+			return true;
+
+	return false;
+}
+
 static inline bool
 pkgconf_fragment_is_special(const char *string)
 {
@@ -61,8 +81,7 @@ pkgconf_fragment_copy_munged(const char *source, unsigned int flags)
 
 	sysroot_dir = pkgconf_tuple_find_global("pc_sysrootdir");
 
-	if (*source != '/' ||
-		(sysroot_dir != NULL && !strncmp(sysroot_dir, source, strlen(sysroot_dir))))
+	if (!pkgconf_fragment_should_munge(source, sysroot_dir))
 		return strdup(source);
 
 	strlcpy(mungebuf, sysroot_dir, sizeof mungebuf);