There's a much better way to handle environment variables. If you come from Ruby on Rails you're used to setting your environment variables in your .ENV file or in your config/application.yml file.
Meteor handles environment variables in a similar way.
Create settings.json file
Inside your server folder in your project, create a file and name it settings.json. Add this file to your gitignore file.
Inside this JSON file, you can save any environment variables you need.
{
  "facebookAppId": "6666667527666666",
  "facebookAppSecret": "00004b20dd845637777321cd3c750000",
  "amazonS3Bucket": "bucket-name"
}
Loading the environment variables
To use these values inside your app during runtime, start Meteor with a --settings option flag.
$ meteor run --settings server/settings.json
Use the values
To use the values, just call the Meteor.settings object.
ServiceConfiguration.configurations.upsert(
  { service: "facebook" },
  {
    $set: {
      appId: Meteor.settings.facebookAppId, 
      secret: Meteor.settings.facebookAppSecret
    }
  }
);
That's all there is to it! Keep your settings safe, and do not commit your keys.