The present study aimed at synthesizing fatty acid methyl esters in a combined enzymatic method by applying degumming and transesterification of soybean oil. A soluble lipase from Serratia sp. W3 and a recombinant phosphatidylcholine‐preferring phospholipase C (PC‐PLC) from Bacillus thuringiensis were used in a consecutive manner for phosphorus removal and conversion into methyl esters. By applying 1% of recombinant PC‐PLC almost 83% of phosphorus was removed (final content of 21.01 mg/kg). Moreover, a sensitive and selective high‐performance liquid chromatography method coupled to tandem mass spectrometry was applied to obtain a comprehensive lipid profile for the simultaneous evaluation of phospholipids removal and diacylglycerol (DAG) increase. A significant increase for all the monitored DAG species, up to 138.42%, was observed by using the enzymatic degumming, in comparison to the crude sample, resulting in an increased oil yield. Serratia sp. W3 lipase was identified as a suitable biocatalyst for biodiesel production, converting efficiently the acylglycerols. The results regarding the physical‐chemical characteristics show that the cetane level, density and pour point of the obtained biodiesel are close to current regulation requirements. These findings highlight the potential of a two‐step process implementation, based on the combination of lipase and phospholipase, as a suitable alternative for biodiesel production.