diff --git a/bazel/emscripten_toolchain/env.bat b/bazel/emscripten_toolchain/env.bat
index c791ff7710..d5b5d5a691 100644
--- a/bazel/emscripten_toolchain/env.bat
+++ b/bazel/emscripten_toolchain/env.bat
@@ -4,3 +4,11 @@ set ROOT_DIR=%EXT_BUILD_ROOT%
 if "%ROOT_DIR%"=="" set ROOT_DIR=%CD%
 set EMSCRIPTEN=%ROOT_DIR%\%EM_BIN_PATH%\emscripten
 set EM_CONFIG=%ROOT_DIR%\%EM_CONFIG_PATH%
+
+:: If EMSDK_PYTHON is a relative path, make it absolute using ROOT_DIR.
+:: This is needed because emscripten system library generation invokes compilers
+:: from subdirectories inside its cache, where relative paths to python break.
+if not "%EMSDK_PYTHON%"=="" ^
+if not "%EMSDK_PYTHON:~1,1%"==":" ^
+if not "%EMSDK_PYTHON:~0,1%"=="\" ^
+	set "EMSDK_PYTHON=%ROOT_DIR%\%EMSDK_PYTHON%"