diff --git a/emsdk b/emsdk
index 660e65a..c77c08f 100755
--- a/emsdk
+++ b/emsdk
@@ -1232,6 +1232,11 @@ JS_ENGINES = [NODE_JS]
   if embedded:
     cfg = cfg.replace(emscripten_config_directory, "' + emsdk_path + '")
 
+  if os.path.exists(dot_emscripten_path()):
+    backup_path = dot_emscripten_path() + ".old"
+    print("Backing up old Emscripten configuration file in " + os.path.normpath(backup_path))
+    move_with_overwrite(dot_emscripten_path(), backup_path)
+
   with open(dot_emscripten_path(), "w") as text_file: text_file.write(cfg)
 
   # Clear old cached emscripten content.
diff --git a/test.py b/test.py
index 4b3713a..c2baf5e 100644
--- a/test.py
+++ b/test.py
@@ -104,7 +104,9 @@ assert not os.path.exists(LIBC)
 print('test tot-upstream')
 check_call('./emsdk install tot-upstream')
 assert not os.path.exists(LIBC)
+old_config = open(os.path.expanduser('~/.emscripten')).read()
 check_call('./emsdk activate tot-upstream')
+assert old_config == open(os.path.expanduser('~/.emscripten.old')).read()
 assert os.path.exists(LIBC), 'activation supplies prebuilt libc' # TODO; test on latest as well
 check_call('upstream/emscripten/emcc hello_world.cpp')
 
@@ -162,4 +164,3 @@ for os, suffix in [
   url = 'https://storage.googleapis.com/webassembly/emscripten-releases-builds/%s/%s/wasm-binaries.%s' % (os, latest_hash, suffix)
   print('  url: ' + url),
   check_call('wget ' + url)
-