MongoDB 3.2 (Released in November 2015) offers an encrypted storage engine. No need to use third party APIs to encrypt your data before insertion or encrypt the whole drive. You can find more details here. However, note that it is only offered for the Enterprise edition only.
It works with the WiredTiger storage engine, which has been the included as an alternative to the default MMAPv1 storage engine since 3.0. If your database is still using MMAPv1, read this guide for the steps to convert a database from MMAPv1 to WiredTiger.
As Fernando Paz noted in the comments, the encrypted storage is only available in MongoDB Enterprise edition.