Microalgal biomass is a prospective substrate for biofuels, also for biogas production. Microalgal treatment of liquid anaerobic digestate and thermophilic anaerobic digestion of microalgal biomass and food waste was studied aiming to improve microalgae – biogas system. Prevalence use of biogas digestate as fertilizer in agriculture is current practice, but due to logistic and agro-technical reasons, it is often separated. Liquid fraction contains a significant portion of nutrients (especially nitrogen and phosphorous), but causes high transport costs or costs of treatment at wastewater treatment plant. The algal treatment technology can present an added value and potential economic benefit for biogas plant. Other benefits of coupling of the technologies are use of CO2 (flue gases) and waste heat. We have tested the efficiency of treatment of liquid digestate as waste water within set pilot system. Results of microalgal treatment of liquid supernatant digestate from thermophilic biogas plant, treating food waste (COD 4.445 ± 973 mg O2 L-1), in algal pond (covered system on 89 m2 with open raceway pond) shows sufficient nitrogen and phosphorous removal and COD reduction efficiency of 81–95 % (COD of effluent reduced to 362 ± 72 mg O2 L- 1) in optimum regime. Digestate organic load on inflow varied 2,317–9,552 mg O2 L-1, and was on average 4,445 ± 973 mg O2 L-1 in optimal regime. Effluent during optimal treatment (treated wastewater) is of such quality, that it can be released to the sewer. The presence of selected pathogens in algal treatment was monitored. Produced microalgal biomass was tested by methane potential assays in thermophilic process. Thermally pretreated microalgae showed higher biomethane potential (from 254.5 ± 35.5 up to 406.1 ± 4,2 mL CH4 g-1 OS), also bioaugmentation of the anaerobic digestion with bacteria C. thermocellum (from 176.4 ± 19.7 to 223.4 ± 5.2mL CH4 g- 1 OS) as native microalgae (from 153.5 ± 32.2 to 168.4 ± 6.0 mL CH4 g-1 OS). Microalgae is good co-substrate with food waste in various combinations (yield from 329.3 ± 6.7 to 497.6 ± 66.5 mL CH4 g-1 OS). Results of this thesis contribute to environment protection with the development of technology for algal treatment of digestate, including technological and economical view on feasibility of thermophilic biogas digestate treatment with microalgae and presents results of efficient pretreatment of produced algal biomass that will accelerate applicability of the solution.