diff --git a/pkgs/development/compilers/cudatoolkit/hooks/setup-cuda-hook.sh b/pkgs/development/compilers/cudatoolkit/hooks/setup-cuda-hook.sh
index 0272e7938b9a..0fa8883081c5 100644
--- a/pkgs/development/compilers/cudatoolkit/hooks/setup-cuda-hook.sh
+++ b/pkgs/development/compilers/cudatoolkit/hooks/setup-cuda-hook.sh
@@ -1,5 +1,8 @@
 # shellcheck shell=bash
 
+# Only run the hook from nativeBuildInputs
+(( "$hostOffset" == -1 && "$targetOffset" == 0)) || return 0
+
 echo Sourcing setup-cuda-hook >&2
 
 extendCUDAToolkit_ROOT() {