The reaction pathway of nitrogen containing compounds under hydrothermal liquefaction (HTL) conditions was investigated by using amino acids as protein model compounds. The effect of organic acids and alkaline catalysts was also investigated by determining the structure and the partition of nitrogen containing species between the resulting solid, aqueous and bio-oil phases. Representative results showed that operating in a water-acetic acid (95/5% v/v) binary solvent system resulted in a dramatic improvement in carbon recovery in the oil phase due to the transformation of water soluble hydrophilic products into oil soluble derivatives by acylation of the amino moiety. The conclusions of this study provide a useful tool to improve the HTL process applied to nitrogen rich biomass, such as the organic fraction of urban waste, sewage sludge, and aquatic biomass (microalgae).