This study aims to design and evaluate the techno-economic feasibility of socially just and context-specific biohubs for producing marine biofuels based on olive residues with hydrothermal liquefaction (HTL) in Spain, using existing infrastructures. The conceptual process and biohubs design are co-designed using a multi-actor approach, involving local stakeholders through participatory methods, with the help of a Capability-sensitive design. The material and energy balances (from Aspen Plus simulations) are used to evaluate the technical and economic performance (such as capital expenses, operational costs, and minimum fuel selling price) of biohub. 21 possible scenarios are investigated to understand the impact of design aspects (such as scale, distributed configuration, and co-processing) on the minimum fuel selling price (MFSP). The MFSP of the HTL biofuels varied by a factor of 0.6–3.1 compared to the conventional fossil-based fuels. Additionally, co-processing of HTL bio-crude at existing petroleum refineries reduces equipment costs by 16%. The study also recommends that the minimum scale of the HTL facilities should be between 588–882 dry tons per day (DTPD) of crude olive pomace processing capacity, to benefit from economies of scale. Overall, the investigation shows an economically feasible way to develop context-relevant olive residue-based biohubs for marine biofuel production with existing infrastructures in Spain, while ensuring social justice near biomass production sites. We argue this approach can be replicated in the other olive-producing regions in the Mediterranean and conclude that olive residues from the Mediterranean region have a huge potential to provide alternative advanced “drop-in” biofuels for the shipping sector.