diff --git a/barretenberg/cpp/bootstrap.sh b/barretenberg/cpp/bootstrap.sh
index 7a38e0bd4f80..3c533971fed9 100755
--- a/barretenberg/cpp/bootstrap.sh
+++ b/barretenberg/cpp/bootstrap.sh
@@ -7,6 +7,7 @@ else
   export native_preset=${NATIVE_PRESET:-clang20-no-avm}
 fi
 export hash=$(hash_str $(../../avm-transpiler/bootstrap.sh hash) $(cache_content_hash .rebuild_patterns))
+export native_build_dir=$(scripts/preset-build-dir $native_preset)
 
 # Injects version number into a given bb binary.
 # Means we don't actually need to rebuild bb to release a new version if code hasn't changed.
diff --git a/barretenberg/cpp/cmake/arch.cmake b/barretenberg/cpp/cmake/arch.cmake
index fe6488cbce3f..ed185b1fa970 100644
--- a/barretenberg/cpp/cmake/arch.cmake
+++ b/barretenberg/cpp/cmake/arch.cmake
@@ -5,11 +5,13 @@ if(WASM)
     add_compile_options(-fno-exceptions -fno-slp-vectorize)
 endif()
 
-# Auto-detect TARGET_ARCH if not explicitly set.
+# Auto-detect TARGET_ARCH if not explicitly set (native builds only).
 # Use 'skylake' on x86_64 (matches our cross-compile presets) and 'generic' on ARM
 # to avoid emitting CPU-specific instructions (e.g. SVE on Graviton) that break on
 # other ARM machines like Apple Silicon.
-if(NOT WASM AND NOT TARGET_ARCH)
+# Skip auto-detection when cross-compiling — the toolchain (e.g. Zig -mcpu) handles
+# architecture targeting, and injecting -march here conflicts with it.
+if(NOT WASM AND NOT TARGET_ARCH AND NOT CMAKE_CROSSCOMPILING)
     if(ARM)
         set(TARGET_ARCH "generic")
     else()