This work proposes the design of a biorefinery process, based on pilot plant information, able to convert waste from Nodipecten nodosus viscera into heparan sulfate (HS), a compound with important biological functions, and applications in wound healing, growth factor regulation, and topical formulations for skin damage. Techno-economic assessments might be conducted through process simulation tools to evaluate the feasibility of implementing large-scale biorefineries facilities, even though the feasibility of biowaste-based biorefineries is limited due to fluctuations in feedstock supply and composition. Process modeling, simulation, and cost evaluation were performed considering raising capacities from 6 to 192 t/y, resulting in HS minimum selling price (MSP) of around 10 % of low molecular weight heparin, a potential commercial competitor. Results indicated that increasing the plant capacity leads to a reduction of around 65 % in the MSP, increasing HS commercial attractiveness. Risk analysis shows similar results for the considered scenarios, mainly due to HS selling price but also to CAPEX estimated uncertainties.