I am having the same issue.

This is built-in browserify behaviour and can not be overridden, an alternative is to add:

{
  "browserify": {
    "transform": ["babelify"]
  }
}

to your node_modules package.json.

In the future please search the issues before creating a new one, thanks! See #44 and #38.

I was having this issue as well, and since Google results for "browserify babel node_modules" comes to this issue, and lots of other issues link here, I'm updating it with details on the other solution (using a global transform), which seems to work better than trying to ask every single modern module I require to add something to their package.json.

After figuring this out through other means, I see it's actually in the FAQ for babelify, so I'm quoting that section here:

Another solution (proceed with caution!) is to run babelify as a global transform. Use the babel ignore option to narrow the number of files transformed:

browserify().transform("babelify", {
  global: true,
  ignore: /\/node_modules\/(?!app\/)/
});

The above example will result in a transform that also includes the app module in node_modules: the global flag transform all files, and the ignore regular expression then excludes all those in the node_modules directory except those that are in node_modules/app (since ?! will match if the given suffix is absent).

In my use, I find the ignore is not required, as for every module that exports ES5 code, babelify is effectively a no-op, and for those that are not, I want it to run them though babelify. Seems safer to opt-out of babelify if it breaks a particular module (which will be noticed in development) rather than need to opt-in (which will only be noticed in production/testing on old browsers).