diff --git a/scripts/build-wxuniversal-wasm.sh b/scripts/build-wxuniversal-wasm.sh
index a31a7eb..4c22111 100755
--- a/scripts/build-wxuniversal-wasm.sh
+++ b/scripts/build-wxuniversal-wasm.sh
@@ -36,6 +36,9 @@ WX_SOURCE="$PROJECT_ROOT/wxwidgets"
 export SHELL="$SCRIPT_DIR/config/config-sub-wrapper.sh"
 export CONFIG_SHELL="$SCRIPT_DIR/config/config-sub-wrapper.sh"
 
+# Disable autom4te cache to keep submodules clean
+export AUTOM4TE="$SCRIPT_DIR/config/autom4te-wrapper.sh"
+
 # Use JOBS from env.sh if set, otherwise use all available cores
 JOBS="${JOBS:-$(nproc 2>/dev/null || sysctl -n hw.ncpu 2>/dev/null || echo 4)}"
 
diff --git a/scripts/config/autom4te-wrapper.sh b/scripts/config/autom4te-wrapper.sh
new file mode 100755
index 0000000..f2a43d6
--- /dev/null
+++ b/scripts/config/autom4te-wrapper.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+# autom4te wrapper - disables cache to keep submodules clean
+# This prevents autom4te.cache directories from being created in source trees
+#
+# Unset AUTOM4TE to prevent infinite recursion when autoconf calls autom4te
+unset AUTOM4TE
+exec autom4te --no-cache "$@"