Abstract Microalgal biomass as a feedstock for biogas production is linked to the parameters biomass productivity and biogas yield. Besides an easy-to-use strain for anaerobic digestion, the photobioreactor (PBR) design is important. A microalgae strain selection revealed Eustigmatos magnus (SAG 36.89) as the most promising strain yielding an average of 100 mg total suspended solids (TSS) L−1 day−1. The strain was tested in cost-effective sleevebag-PBR-systems of 10 cm, 20 cm and 30 cm diameter facing the light from the front or laterally. Highest mean productivity on a volumetric basis was measured in PBRs with the lowest diameter (104 and 117 mg L−1 day−1. The highest productivity per m−2 was achieved in 10 cm PBRs with front light configuration (9.35 g TSS m−2 day−1). The lateral light configuration of 10 cm PBRs had positive aspects such as the lowest mean water demand to produce 1 kg TSS (481 L−1 kg−1) and the lowest mean energy demand for medium separation of 1 kg TSS (106 Wh). The concentrated microalgal biomass was then subjected to ultrasonication and thermal pre-treatment (90 °C and 120 °C) and tested in BMP tests. Mesophilic anaerobic mono-digestion of untreated microalgae biomass led to a methane (CH4) yield of 343 L−1 kg−1 volatile solids (VS). Thermal pre-treatment at 120 °C resulted in significantly increased CH4 yields of 430 L−1 kg−1 VS. As thermal pre-treatment can be easily installed nearby a biogas plant it could be an interesting option for AD of microalgal biomass with only little investment.