The disclosure provides methods and systems for the production of biodiesel from biological feedstocks such as vegetable oils or animal fats. In particular, the disclosure is directed to the product of biodiesel from seeds such as non-edible oil seeds. Methods for maximizing oil recovery from the feedstocks are provided, as well as methods to convert free fatty acids in the feedstocks into glycerides amenable to transesterification. Thus the methods and systems provide for efficient biodiesel production.