Microalgal biomass can potentially be valorized for several purposes, targeting either high added-value metabolites or biofuels. In case the cultivation conditions are inappropriate for the production of high-value metabolites, or the produced yields are insufficient for extraction and further valorization, there is the alternative of the anaerobic digestion (AD) process for biogas production. In the current study, Chlorella vulgaris biomass was treated through the process of AD, focusing on the effect of fatty acids (FAs) content (5–30 %) on biomethane production. Mixotrophic and heterotrophic conditions were used to produce biomass samples with different FAs content. The biochemical methane potential (BMP) assays of the biomass samples followed, targeting the evaluation of the process, taking into account the FAs concentration effect. The BMP yields varied between 304 (5 % FAs) and 502 NmL CH4 gVSadded−1 (30 % FAs). The next step in this work was the mathematical modeling of CH4 production, where the proposed model could satisfactorily simulate the biological process with R2 = 0.94 for all the studied experiments. Such a model can be a valuable tool for deciding on the most appropriate biomass utilization option and the description of AD with dual-stage CH4 production.