Oxidation can not truly be prevented, but the process can be significantly slowed, by use of antioxidants. Antioxidants are compounds which interrupt the oxidation process by preferentially reacting with the fat radical to from a stable radical which does not quickly react with oxygen. Antioxidants serve to stall the propagation phase of the oxidation cycle. Antioxidants cannot "fix" oxidized materials. They are only effective if they are added early in the life of biodiesel. Antioxidants are virtually ineffective in retarding deterioration of biodiesel when added to already oxidized systems.

In addition, certain compounds are found to work with the antioxidant to further retard the oxidation process. The initiation phase of the oxidation process may be catalyzed by metal ions. Chelating agents bind metal ions making them unavailable for catalyzing the initiation phase, thus slowing oxidation process.