diff --git a/tools/bpf/resolve_btfids/main.c b/tools/bpf/resolve_btfids/main.c
index cd42977c6a1f4e..ef0764d6891e43 100644
--- a/tools/bpf/resolve_btfids/main.c
+++ b/tools/bpf/resolve_btfids/main.c
@@ -90,6 +90,14 @@
 
 #define ADDR_CNT	100
 
+#if __BYTE_ORDER == __LITTLE_ENDIAN
+# define ELFDATANATIVE	ELFDATA2LSB
+#elif __BYTE_ORDER == __BIG_ENDIAN
+# define ELFDATANATIVE	ELFDATA2MSB
+#else
+# error "Unknown machine endianness!"
+#endif
+
 struct btf_id {
 	struct rb_node	 rb_node;
 	char		*name;
@@ -117,6 +125,7 @@ struct object {
 		int		 idlist_shndx;
 		size_t		 strtabidx;
 		unsigned long	 idlist_addr;
+		int		 encoding;
 	} efile;
 
 	struct rb_root	sets;
@@ -320,6 +329,7 @@ static int elf_collect(struct object *obj)
 {
 	Elf_Scn *scn = NULL;
 	size_t shdrstrndx;
+	GElf_Ehdr ehdr;
 	int idx = 0;
 	Elf *elf;
 	int fd;
@@ -351,6 +361,13 @@ static int elf_collect(struct object *obj)
 		return -1;
 	}
 
+	if (gelf_getehdr(obj->efile.elf, &ehdr) == NULL) {
+		pr_err("FAILED cannot get ELF header: %s\n",
+			elf_errmsg(-1));
+		return -1;
+	}
+	obj->efile.encoding = ehdr.e_ident[EI_DATA];
+
 	/*
 	 * Scan all the elf sections and look for save data
 	 * from .BTF_ids section and symbols.
@@ -681,6 +698,24 @@ static int sets_patch(struct object *obj)
 			 */
 			BUILD_BUG_ON(set8->pairs != &set8->pairs[0].id);
 			qsort(set8->pairs, set8->cnt, sizeof(set8->pairs[0]), cmp_id);
+
+			/*
+			 * When ELF endianness does not match endianness of the
+			 * host, libelf will do the translation when updating
+			 * the ELF. This, however, corrupts SET8 flags which are
+			 * already in the target endianness. So, let's bswap
+			 * them to the host endianness and libelf will then
+			 * correctly translate everything.
+			 */
+			if (obj->efile.encoding != ELFDATANATIVE) {
+				int i;
+
+				set8->flags = bswap_32(set8->flags);
+				for (i = 0; i < set8->cnt; i++) {
+					set8->pairs[i].flags =
+						bswap_32(set8->pairs[i].flags);
+				}
+			}
 		}
 
 		pr_debug("sorting  addr %5lu: cnt %6d [%s]\n",