diff --git a/tools/lib/bpf/linker.c b/tools/lib/bpf/linker.c
index 7489306cd6f7..9bf218db443e 100644
--- a/tools/lib/bpf/linker.c
+++ b/tools/lib/bpf/linker.c
@@ -135,6 +135,7 @@ struct bpf_linker {
 	int fd;
 	Elf *elf;
 	Elf64_Ehdr *elf_hdr;
+	bool swapped_endian;
 
 	/* Output sections metadata */
 	struct dst_sec *secs;
@@ -324,13 +325,8 @@ static int init_output_elf(struct bpf_linker *linker, const char *file)
 
 	linker->elf_hdr->e_machine = EM_BPF;
 	linker->elf_hdr->e_type = ET_REL;
-#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
-	linker->elf_hdr->e_ident[EI_DATA] = ELFDATA2LSB;
-#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__
-	linker->elf_hdr->e_ident[EI_DATA] = ELFDATA2MSB;
-#else
-#error "Unknown __BYTE_ORDER__"
-#endif
+	/* Set unknown ELF endianness, assign later from input files */
+	linker->elf_hdr->e_ident[EI_DATA] = ELFDATANONE;
 
 	/* STRTAB */
 	/* initialize strset with an empty string to conform to ELF */
@@ -541,19 +537,21 @@ static int linker_load_obj_file(struct bpf_linker *linker, const char *filename,
 				const struct bpf_linker_file_opts *opts,
 				struct src_obj *obj)
 {
-#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
-	const int host_endianness = ELFDATA2LSB;
-#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__
-	const int host_endianness = ELFDATA2MSB;
-#else
-#error "Unknown __BYTE_ORDER__"
-#endif
 	int err = 0;
 	Elf_Scn *scn;
 	Elf_Data *data;
 	Elf64_Ehdr *ehdr;
 	Elf64_Shdr *shdr;
 	struct src_sec *sec;
+	unsigned char obj_byteorder;
+	unsigned char *link_byteorder = &linker->elf_hdr->e_ident[EI_DATA];
+#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
+	const unsigned char host_byteorder = ELFDATA2LSB;
+#elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__
+	const unsigned char host_byteorder = ELFDATA2MSB;
+#else
+#error "Unknown __BYTE_ORDER__"
+#endif
 
 	pr_debug("linker: adding object file '%s'...\n", filename);
 
@@ -579,11 +577,25 @@ static int linker_load_obj_file(struct bpf_linker *linker, const char *filename,
 		pr_warn_elf("failed to get ELF header for %s", filename);
 		return err;
 	}
-	if (ehdr->e_ident[EI_DATA] != host_endianness) {
+
+	/* Linker output endianness set by first input object */
+	obj_byteorder = ehdr->e_ident[EI_DATA];
+	if (obj_byteorder != ELFDATA2LSB && obj_byteorder != ELFDATA2MSB) {
 		err = -EOPNOTSUPP;
-		pr_warn_elf("unsupported byte order of ELF file %s", filename);
+		pr_warn("linker: unknown byte order of ELF file %s\n", filename);
 		return err;
 	}
+	if (*link_byteorder == ELFDATANONE) {
+		*link_byteorder = obj_byteorder;
+		linker->swapped_endian = obj_byteorder != host_byteorder;
+		pr_debug("linker: set %s-endian output byte order\n",
+			 obj_byteorder == ELFDATA2MSB ? "big" : "little");
+	} else if (*link_byteorder != obj_byteorder) {
+		err = -EOPNOTSUPP;
+		pr_warn("linker: byte order mismatch with ELF file %s\n", filename);
+		return err;
+	}
+
 	if (ehdr->e_type != ET_REL
 	    || ehdr->e_machine != EM_BPF
 	    || ehdr->e_ident[EI_CLASS] != ELFCLASS64) {
@@ -1111,6 +1123,27 @@ static bool sec_content_is_same(struct dst_sec *dst_sec, struct src_sec *src_sec
 	return true;
 }
 
+static bool is_exec_sec(struct dst_sec *sec)
+{
+	if (!sec || sec->ephemeral)
+		return false;
+	return (sec->shdr->sh_type == SHT_PROGBITS) &&
+	       (sec->shdr->sh_flags & SHF_EXECINSTR);
+}
+
+static int exec_sec_bswap(void *raw_data, int size)
+{
+	const int insn_cnt = size / sizeof(struct bpf_insn);
+	struct bpf_insn *insn = raw_data;
+	int i;
+
+	if (size % sizeof(struct bpf_insn))
+		return -EINVAL;
+	for (i = 0; i < insn_cnt; i++, insn++)
+		bpf_insn_bswap(insn);
+	return 0;
+}
+
 static int extend_sec(struct bpf_linker *linker, struct dst_sec *dst, struct src_sec *src)
 {
 	void *tmp;
@@ -1170,6 +1203,16 @@ static int extend_sec(struct bpf_linker *linker, struct dst_sec *dst, struct src
 		memset(dst->raw_data + dst->sec_sz, 0, dst_align_sz - dst->sec_sz);
 		/* now copy src data at a properly aligned offset */
 		memcpy(dst->raw_data + dst_align_sz, src->data->d_buf, src->shdr->sh_size);
+
+		/* convert added bpf insns to native byte-order */
+		if (linker->swapped_endian && is_exec_sec(dst)) {
+			err = exec_sec_bswap(dst->raw_data + dst_align_sz,
+					     src->shdr->sh_size);
+			if (err) {
+				pr_warn("%s: error changing insns endianness\n", __func__);
+				return err;
+			}
+		}
 	}
 
 	dst->sec_sz = dst_final_sz;
@@ -2630,6 +2673,14 @@ int bpf_linker__finalize(struct bpf_linker *linker)
 		if (!sec->scn)
 			continue;
 
+		/* restore sections with bpf insns to target byte-order */
+		if (linker->swapped_endian && is_exec_sec(sec)) {
+			err = exec_sec_bswap(sec->raw_data, sec->sec_sz);
+			if (err) {
+				pr_warn("error finalizing insns endianness\n");
+				return libbpf_err(err);
+			}
+		}
 		sec->data->d_buf = sec->raw_data;
 	}
 
@@ -2696,6 +2747,13 @@ static int emit_elf_data_sec(struct bpf_linker *linker, const char *sec_name,
 	return 0;
 }
 
+static enum btf_endianness
+linker_btf_endianness(const struct bpf_linker *linker)
+{
+	unsigned char byteorder = linker->elf_hdr->e_ident[EI_DATA];
+	return byteorder == ELFDATA2MSB ? BTF_BIG_ENDIAN : BTF_LITTLE_ENDIAN;
+}
+
 static int finalize_btf(struct bpf_linker *linker)
 {
 	LIBBPF_OPTS(btf_dedup_opts, opts);
@@ -2742,6 +2800,22 @@ static int finalize_btf(struct bpf_linker *linker)
 		return err;
 	}
 
+	/* Set .BTF and .BTF.ext output byte order */
+	err = btf__set_endianness(linker->btf,
+				  linker_btf_endianness(linker));
+	if (err) {
+		pr_warn("failed to set .BTF output endianness: %d\n", err);
+		return err;
+	}
+	if (linker->btf_ext) {
+		err = btf_ext__set_endianness(linker->btf_ext,
+					      linker_btf_endianness(linker));
+		if (err) {
+			pr_warn("failed to set .BTF.ext output endianness: %d\n", err);
+			return err;
+		}
+	}
+
 	/* Emit .BTF section */
 	raw_data = btf__raw_data(linker->btf, &raw_sz);
 	if (!raw_data)
