Abstract The interest in third generation biofuels from microalgae has been rising during the past years. Meanwhile, it seems not economically feasible to grow algae just for biofuels. Co-products with a higher value should be produced by extracting a particular algae fraction to improve the economics of an algae biorefinery. The present study aims at analyzing the influence of two main microalgae components (lipids and proteins) on the composition and quantity of biocrude oil obtained via hydrothermal liquefaction of two strains (Nannochloropsis gaditana and Scenedesmus almeriensis). The algae were liquefied as raw biomass, after extracting lipids and after extracting proteins in microautoclave experiments at different temperatures (300 to 375 °C) for 5 and 15 min. The results indicate that extracting the proteins from the microalgae prior to HTL may be interesting to improve the economics of the process while at the same time reducing the nitrogen content of the biocrude oil.