The efficient production of biodiesel in hydrophobic ionic liquids using immobilized lipase was demonstrated. The use of ionic liquids containing long alkyl chains on the cation has the important advantage of producing homogeneous systems at the start of the reaction but, when the reaction is complete, a three-phase system is created that allows selective extraction of the products using straightforward separation techniques, while the ionic liquid and the enzyme can be reused. Fifteen ionic liquids based on different alkyl chain length of the methyl imidazolium cation ([C₁₀MIM], [C₁₂MIM], [C₁₄MIM], [C₁₆MIM] and [C₁₈MIM]) combined with [BF₄], [PF₆] or [NTf₂] anions were assayed as reaction media for two immobilized lipases (Candida antarctica lipase B and Pseudomonas fluorescens lipase AK) for biodiesel production. The highest synthetic activity was obtained in [C₁₆MIM] [NTf₂] using Novozym 435 (immobilized Candida antarctica lipase with 245.13 U g⁻¹ IME), its activity being more than three times higher than in a solvent-free system. Additionally, in this IL the fatty acid methyl esters production was 90.29% after 3 h, while in the solvent-free system it was 27.3%. The influence of several reaction parameters, such as temperature, methanol-to-oil molar ratio, alkyl-chain length of the alcohols, IL:substrate volume ratios, amount of enzyme, and oils feedstock were studied and optimized.