The greenhouse gases methane (CH4) and carbon dioxide (CO2) are end products of microbial anaerobic degradation of organic matter (OM) in lake sediments. Although previous research has shown that phytoplankton lipid content influences sediment methanogenesis, current understanding on how OM quality affects methanogenesis is still limited. Such information is needed to more accurately assess how lake greenhouse gas emissions may change in response to anthropogenic activities. We cultured 11 phytoplankton species from five classes and studied how taxonomic identity, C : N ratio, lipid content, and fatty acid composition of phytoplankton biomass affects the CH4 and net CO2 production in anaerobic lake sediments with an incubation experiment that lasted > 100 d. The carbon‐normalized potential CH4 (0.09–0.23 μmol mg C−1 d−1) and net CO2 (0.09–0.28 μmol mg C−1 d−1) production rates were not related to phytoplankton taxonomic affiliation (e.g., class, species), C : N ratio, or fatty acid composition of algal biomass. Methane or net CO2 production potentials did not increase with higher lipid content (10–30%); however, total fatty acid content had a weak correlation with CH4 production potential. In contrast to previous research, our results suggest that lipid content is of minor importance in determining methanogenesis rates from the biomass of multispecies phytoplankton communities settling on sediments. The decrease in CO2 concentration and the correlation between stable carbon isotope signatures of CH4 and molar ratio of CH4 and CO2 at the end of the experiment may indicate that importance of hydrogenotrophic methanogenesis, which uses CO2 when other substrates become limiting, increased during the long incubation.