AbstractThe aim of this study was the evaluation of two different procedures for the one‐pot transformation of oil extracted from Citrus limon seeds to a mixture of fatty acid methyl esters (FAMEs) and glycerol derivatives for application as a potential biofuel. Lemon seed oil was obtained by Soxhlet extraction. The first procedure was realized by efficient irreversible transesterification of the oil in hexane by lipase B from Candida antarctica (Novozym 435®) using dimethyl carbonate as the alcohol donor. For the realization of the second methodology an acid‐catalyzed transformation was carried out, dissolving the seed oil in methyl tert‐butyl ether in a microwave tube using Amberlyst®‐36 dry form catalyst. Both procedures, in optimized conditions, led to the complete conversion of the triglycerides to give the corresponding FAMEs and a mixture of glycerol derivatives. The absence of free glycerol in the final mixtures makes the two herein described procedures considerably advantageous in terms of both cost and sustainability since they enable performance of the production of FAMEs without requiring steps to remove glycerol. These final mixtures may be used in the energy chain and exploited as biofuels. © 2022 The Authors. Biofuels, Bioproducts and Biorefining published by Society of Industrial Chemistry and John Wiley & Sons, Ltd.