To obtain drop-in fuel properties from 3rd generation biomass, we herein report the catalytic hydrotreatment of microalgae biocrude, produced from hydrothermal liquefaction (HTL) of Spirulina. Our contribution focuses on the effect of temperature, initial H2 pressure, and residence time on the removal of heteroatoms (O and N) in a batch hydrotreating setup. In contrast to common experimental protocols for hydrotreating at batch scale, we devised a set of two-level factorial experiments and studied the most influential parameters affecting the removal of heteroatoms. It was found that up to 350 °C, the degree of deoxygenation (de-O) is mainly driven by temperature, whereas the degree of denitrogenation (de-N) also relies on initial H2 pressure and temperature-pressure interaction. Based on this, complete deoxygenation was obtained at mild operating conditions (350 °C), reaching a concurrent 47% denitrogenation. Moreover, three optimized experiments are reported with 100% removal of oxygen. In addition, the analysis by GC-MS and Sim-Dis gives insight to the fuel quality. The distribution of heteroatom N in lower (<340 °C) and higher (>340 °C) fractional cuts is studied by a fractional distillation unit following ASTM D-1160. Final results show that 63–68% of nitrogen is concentrated in higher fractional cuts.