BACKGROUND: Lipid extraction is a major bottleneck for the commercialization of microalgae due to energy costs involved during solvent recycling. Direct transesterification offers the possibility to bypass the extraction step by immediately converting the lipids to fatty acid methyl esters (FAMEs). In this study, the efficiency of direct transesterification after pulsed electric field (PEF) treatment was evaluated. Freshly harvested Auxenochlorella protothecoides (A. protothecoides), cultivated either autotrophically or mixotrophically, was subjected to PEF. Two treatment energies were tested, 0.25 and 1.5 MJ kg dw −1 , and results were compared with those for conventional two-step transesterification.RESULTS: For autotrophically grown A. protothecoides, the percentage of the total FAMEs recovered from untreated biomass and microalgae treated with 0.25 MJ kg dw −1 was 30% for both cases, while for 1.5 MJ kg dw −1 it was 65%. A 24 h incubation step between PEF treatment and direct transesterification significantly improved the results. Untreated biomass remained stable with 30% of FAMEs, while with both treatment energies a 97% FAME recovery was achieved. However, for mixotrophic A. protothecoides the process was not as effective. Approximately 30% of FAMEs were recovered for all three conditions immediately after PEF with only a marginal increase after incubation. The reason for this different behavior of the two cultivation modes is unknown and under investigation. CONCLUSIONS: Overall, the synergy between PEF and direct transesterification was proven to have potential, in particular for autotrophic microalgae. Its implementation and further optimization in a biorefinery therefore merit further attention.