Oxylipins are metabolites derived from lipid peroxidation. The plant oxylipin methyl jasmonate (MJ) shows cytotoxic activity against cancer cell lines of various origins, with ATP-depletion being one of the mechanisms responsible for this effect. The cytotoxic activity of oxylipins (OXLs) isolated from the microalgae Chlamydomonas debaryana (13-HOTE) and Nannochloropsis gaditana (15-HEPE) was higher against UACC-62 (melanoma) than towards HT-29 (colon adenocarcinoma) cells. OXLs lowered the ATP levels of HT-29 and UACC-62 cells, but the effect was higher on the second cell line, which had higher basal ATP. This result proves a link between the cytotoxicity and the capability of these compounds to deplete ATP. In addition, the combination of 13-HOTE with the anticancer drug 5-fluorouracil (5-FU) induced a synergistic toxicity against HT-29 cells. These results highlight the therapeutic potential of oxylipins derived from microalgae.