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The effect of direct transesterification methods on the omega-3/6 composition of extracts from Phaeodactylum tricornutum was studied. The aim of this work was to identify an extraction method which allowed to obtain the most suitable profile of fatty acids in terms of its potential benefits to health, particularly if further used in the food industry. Seven methods using acids, alkalis, and heterogeneous-catalysts, (namely methods from 1 to 7, abbreviated as M1-M7) were performed to determine α-linolenic (ALA), linoleic (LA), docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids. The composition of fatty acids was in all cases characterized by the major abundance of palmitic (23.95–34.08%), palmitoleic (30.94–35.56%), oleic acids (3.00–7.41%), and EPA (0.5–6.45%). Unsaturated fatty acids extraction yield was higher with a two-step transesterification process (M6, 63.65%). The total fatty acid methyl ester content (FAME) obtained with acid-transesterification (M1) reached about 21% wt, and 60% w/w total lipids. ALA higher relative content (ALA/LA ratio) was obtained when a lipid pre-extraction step was performed prior to acid-catalysis (M4). The transesterification method based on alkali-catalyst (M3, KOH catalyst) led to obtain higher DHA relative contents (DHA/EPA ratio up to 0.11), although its FAME content was 3.75-fold lower than that obtained with acid-transesterification (M1). Overall, this study shows that direct transesterification with alkali-catalyst (M3) improves the determination of PUFA content from the diatom through a more efficient transesterification-based extraction process, and thus allow to assess the value of the biomass more accurately for application in the food industry.