The use of ozone-air flotation for microalgae harvesting was investigated, in terms of its environmental feasibility and use in catalytic HTL. The environmental feasibility was determined by the Net Energy Ratio (NER) and carbon footprint metrics following a life cycle assessment (LCA). The effect of the variables in the catalytic HTL process (catalyst load, temperature, time), on the distribution of bio-crude and hydrocarbons, was experimentally evaluated using a mixed microalgae culture dominated by Scenedesmus sp. grown in wastewater and harvested by ozone-air flotation or gravity-sedimentation, respectively. Liquefaction was carried at three temperatures (325 °C, 350 °C and 370 °C), three reaction times (30, 60 and 120 min) and two HZSM-5 catalyst loads (0, 5 and 7 wt%). The bio-crude yields obtained (17 to 20%) were similar with both harvesting methods; however, the production of aliphatic compounds was doubled, when using ozone-air flotation, and further increased when using a HZMS-5 catalyst. The highest bio-crude quality (N: 3.0%, O: 5.6%, S: 0.1%) and high heat values (42.3 MJ/kg) were produced at 325 °C, 60 min and 5 wt%, in contrast with sedimented microalgae (6.0%, 7.0%, 1.0%, and 39.3 MJ/kg, respectively). Energy and carbon footprint were quantified with a LCA approach for a scenario using a functional unit (FU) of 1 GJ of bio-crude production and its possible bio-jet fuel conversion as a potential product. HTL microalgae conversion required the highest amount of energy among evaluated cultivation and harvesting processes. Harvesting via ozone-air flotation, gave a NER value and carbon footprint of 2.7 and 30.5 kg CO2 eq/GJ of bio-jet fuel, respectively. The proposed novel system had significantly lower greenhouse gas equivalent emissions (by 65%) and NER values (by 48%) than for conventional jet fuel.