This work assesses scale effects in designing a biorefinery from Sargassum muticum seaweed by applying a detailed process modeling methodology. Two process conversion units were simulated: one considering anaerobic digestion steps for producing biogas and generating electricity (base project), and the other with residual seaweed solids sold as fertilizer (alternative project). A comprehensive economic analysis was performed to estimate the minimum selling price of the process's main product (fucoidan extract). Results indicated that capital expenditures are up to 12.7% times higher in the base project. Minimum selling prices of the fucoidan extract product demonstrate the biorefinery’s economies of scale for both projects. Seaweed’s low methane potential reduces the economic attractiveness of electricity generation from biogas in the base project. Conversely, organic fertilizer price was more influential in the alternative project. Nonetheless, risk analyses show similar results for both scenarios, mainly due to fucoidan extract selling price and CAPEX estimates uncertainties.