diff --git a/Makefile.envs b/Makefile.envs
index 17457a851..8fd24c099 100644
--- a/Makefile.envs
+++ b/Makefile.envs
@@ -114,6 +114,8 @@ export MAIN_MODULE_LDFLAGS= $(LDFLAGS_BASE) \
 	-s POLYFILL \
 	-s MIN_SAFARI_VERSION=140000 \
 	-s STACK_SIZE=5MB \
+	-s AUTO_JS_LIBRARIES=0 \
+	-s AUTO_NATIVE_LIBRARIES=0 \
 	\
 	-lpython$(PYMAJOR).$(PYMINOR) \
 	-lffi \
diff --git a/docs/project/changelog.md b/docs/project/changelog.md
index 3aa4a2440..aa3b0adc7 100644
--- a/docs/project/changelog.md
+++ b/docs/project/changelog.md
@@ -31,6 +31,12 @@ myst:
 - {{ Enhancement }} Updated Emscripten to version 3.1.31
   {pr}`3471`, {pr}`3517`
 
+- {{ Breaking }} Following libraries are now not linked to the Pyodide main module:
+  `libgl`, `libal`, `libhtml5`. This normally shouldn't affect users, but if you
+  are using these libraries in a package that are built out-of-tree, you will
+  need to link them to the package manually.
+  {pr}`3505`
+
 ### Build System
 
 - {{ Enhancement }} Improved logging in `pyodide-build` with rich.