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Forestry's second aim is to add alternate fuel sources for its own engines, as well as IC2 and BC engines. Currently three fuels are available:

• Seed Oil: A weaker fuel than Biomass, for use in Forestry's Biogas Engines.
• Liquid Biomass: For fueling Forestry's own Biogas Engines and Bio Generators.
• Biofuel: For fueling BC Combustion Engines or Forestry's Bio Generators. Can also be used to fill Fuel Cans for IC2.

In order to get seed oil, seeds must be put into a Squeezer. The basis for biofuel is liquid biomass. Biomass is created by fermenting surplus saplings from tree farms in a Fermenter using Fertilizer, Compost or Mulch. To create biofuel, biomass needs to be distilled using a Still.

The resulting seed oil, biomass, or biofuel can either be used directly in engines or be filled into empty cans from Forestry or into empty fuel cans for use in IndustrialCraft2 using a Bottler.