Acid catalysts were prepared by sulfonation of carbon materials obtained from the pyrolysis of sugar beet molasses, a cheap, viscous byproduct in the processing of sugar beets into sugar. Conditions for the pyrolysis of molasses (temperature and time) influenced catalyst performance; the best combination came from pyrolysis at low temperature (420 °C) for a relatively long time (8–15 h), which ensured better stability of the final material. The most effective molasses catalyst was highly active in the esterification of fatty acids with methanol (100 % yield after 3 h) and more active than common solid acidic catalysts in the transesterification of vegetable oils with 25–75 wt % of acid content (55–96 % yield after 8 h). A tandem process using a solid acid molasses catalyst and potassium hydroxide in methanol was developed to de-acidificate and transesterificate algal oils from Chlamydomonas reinhardtii, Nannochloropsis gaditana, and Phaeodactylum tricornutum, which contain high amounts of free fatty acids. The amount of catalyst required for the de-acidification step was influenced by the chemical composition of the algal oil, thus operational conditions were determined not only in relation to free fatty acids content in the oil, but according to the composition of the lipid extract of each algal species.