diff --git a/toolchain/toolchain-common.in b/toolchain/toolchain-common.in
index 5611b5bbe8..ff667c0b25 100644
--- a/toolchain/toolchain-common.in
+++ b/toolchain/toolchain-common.in
@@ -403,11 +403,14 @@ config BR2_TOOLCHAIN_HAS_SYNC_8
 	default y if BR2_TOOLCHAIN_X86_HAS_SYNC_8
 
 # libatomic is available since gcc 4.8, when thread support is
-# enabled.
+# enabled. Also, libatomic doesn't recognize "uclinux" as a valid OS
+# part of the tuple, and is therefore not build on uclinux targets,
+# which is why BR2_BINFMT_FLAT configurations are excluded.
 config BR2_TOOLCHAIN_HAS_LIBATOMIC
 	bool
 	default y if BR2_TOOLCHAIN_GCC_AT_LEAST_4_8 && \
-		BR2_TOOLCHAIN_HAS_THREADS
+		BR2_TOOLCHAIN_HAS_THREADS && \
+		!BR2_BINFMT_FLAT
 
 # __atomic intrinsics are available:
 # - with gcc 4.8, either through built-ins or libatomic, on all