diff --git a/pkgs/development/compilers/binaryen/default.nix b/pkgs/development/compilers/binaryen/default.nix
index d521ff984c1c..c6c86cecc7a8 100644
--- a/pkgs/development/compilers/binaryen/default.nix
+++ b/pkgs/development/compilers/binaryen/default.nix
@@ -41,6 +41,12 @@ stdenv.mkDerivation rec {
       sed -i '/gtest/d' third_party/CMakeLists.txt
       rmdir test/spec/testsuite
       ln -s ${testsuite} test/spec/testsuite
+      # scripts/test/lld.py checks `'64' in input_path` to enable the
+      # memory64/bigint flags; the full Nix build path leaks digits that
+      # can accidentally contain "64", wrongly triggering those flags for
+      # non-memory64 tests (e.g. duplicate_imports.wat). Match on basename.
+      substituteInPlace scripts/test/lld.py \
+        --replace-fail "'64' in input_path" "'64' in os.path.basename(input_path)"
     else
       cmakeFlagsArray=($cmakeFlagsArray -DBUILD_TESTS=0)
     fi