Short answer: yes
Long answer: it depends.
According to Volkswagen, the folks that designed and built your car, up to 5% biofuels are acceptable.
The engine will run fine on B100 however. But keep in mind, the term 'biodiesel' often gets confused with 'waste vegetable oil'.
Biodiesel is diesel fuel made from various [renewable] sources, usually plant stocks such as soybean oil. #2 diesel is also diesel fuel but is made from petroleum (the stuff pumped out of the Earth from dead organisms from millions of years ago).
Waste vegetable oil is NOT diesel fuel. Although a diesel engine CAN burn it, there are some risks involved, and you can do a search here as well as the wonderful internet and read all about it.