diff --git a/libpkgconf/fragment.c b/libpkgconf/fragment.c
index f41d304..03b2709 100644
--- a/libpkgconf/fragment.c
+++ b/libpkgconf/fragment.c
@@ -55,17 +55,28 @@ pkgconf_fragment_copy_munged(const char *source, unsigned int flags)
 {
 	char mungebuf[PKGCONF_BUFSIZE];
 	char *sysroot_dir;
+	bool isystem = false;
 
 	if (!(flags & PKGCONF_PKG_PKGF_MUNGE_SYSROOT_PREFIX))
 		return strdup(source);
 
+	if (strncmp(source, "-isystem ", 9) == 0) {
+		isystem = true;
+		source+=9;
+	}
+
 	sysroot_dir = pkgconf_tuple_find_global("pc_sysrootdir");
 
 	if (*source != '/' ||
 		(sysroot_dir != NULL && !strncmp(sysroot_dir, source, strlen(sysroot_dir))))
 		return strdup(source);
 
-	strlcpy(mungebuf, sysroot_dir, sizeof mungebuf);
+	if (isystem) {
+		strlcpy(mungebuf, "-isystem ", sizeof mungebuf);
+	} else {
+		strlcpy(mungebuf, "", sizeof mungebuf);
+	}
+	strlcat(mungebuf, sysroot_dir, sizeof mungebuf);
 	strlcat(mungebuf, source, sizeof mungebuf);
 
 	return strdup(mungebuf);
@@ -109,7 +120,11 @@ pkgconf_fragment_add(pkgconf_list_t *list, const char *string, unsigned int flag
 		frag = calloc(sizeof(pkgconf_fragment_t), 1);
 
 		frag->type = 0;
-		frag->data = strdup(string);
+		if (strncmp(string, "-isystem ", 9) == 0) {
+			frag->data = pkgconf_fragment_copy_munged(string, flags);
+		} else {
+			frag->data = strdup(string);
+		}
 	}
 
 	pkgconf_node_insert_tail(&frag->iter, frag, list);
@@ -226,12 +241,24 @@ pkgconf_fragment_parse(pkgconf_list_t *list, pkgconf_list_t *vars, const char *v
 {
 	int i, argc;
 	char **argv;
+	char modified_arg[PKGCONF_BUFSIZE];
 	char *repstr = pkgconf_tuple_parse(vars, value);
 
 	pkgconf_argv_split(repstr, &argc, &argv);
 
-	for (i = 0; i < argc; i++)
-		pkgconf_fragment_add(list, argv[i], flags);
+	for (i = 0; i < argc; i++) {
+		if (strcmp(argv[i], "-I") == 0 || strcmp(argv[i], "-L") == 0) {
+			snprintf(modified_arg, sizeof(modified_arg), "%s%s", argv[i], argv[i+1]);
+			pkgconf_fragment_add(list, modified_arg, flags);
+			i++;
+		} else if (strcmp(argv[i], "-isystem") == 0) {
+			snprintf(modified_arg, sizeof(modified_arg), "%s %s", argv[i], argv[i+1]);
+			pkgconf_fragment_add(list, modified_arg, flags);
+			i++;
+		} else {
+			pkgconf_fragment_add(list, argv[i], flags);
+		}
+	}
 
 	pkgconf_argv_free(argv);
 	free(repstr);