Microalgae are regarded as a promising source of lipids for bio-diesel production and bio-products. The current paper investigates the processing of microalgal slurries under controlled microwave irradiation. Microwave power was applied to reach temperatures of 80, 100, 120 and 140. °C at a constant residence time of 12. min. Microwave irradiation led to disruption of the algal cell walls which facilitated lipid extraction. The influence of inorganic material on microwave heating was assessed for three strains including, Nannochloropsis occulata, Chlorogloeopsis fritschii and Pseudochoricystis ellipsoidea. Mass balances were calculated and showed that the amount of carbon, nitrogen and total mass recovered in the residue was highly dependent on process conditions and algae strain. Hydrothermal microwave processing (HMP) was found to be an effective pre-treatment for hydrothermal liquefaction and extraction of lipids and phytochemicals.