Biomethane from anaerobic digestion of agricultural feedstock is a versatile energy vector for decarbonising agriculture, heavy transport and heat. To lower costs and increase the emission-savings potential, photosynthetic biogas upgrading, cogenerating microalgae with biomethane is investigated here. In a first-of-its-kind work, this paper reports the enviro-economic performance and the marginal (CO2) abatement cost (MAC) of a polygeneration plant co-producing energy (biomethane), food (Spirulina powder) and bio-fertiliser (digestate) from agricultural feedstock using photosynthetic biogas upgrading at small, medium, and industrial scales. A negative MAC at industrial scale (3 MW biomethane), highlighted the environmental and economic benefit (net present value > 11.5 million€ and internal rate of return >40%) of the process as a low-carbon technology over conventional biomethane production processes at a biomethane sale price of 3 c€/kWh (comparable to natural gas). The operational expenditure, including the cost of the Spirulina cultivation medium and the plant capacity factor had the highest influence on its profitability. Replacing beef as a complete food with Spirulina powder maximised the emission savings rather than replacing beef protein with Spirulina protein. Economic allocation as opposed to energy allocation ensured that the levelised cost and specific greenhouse gas emissions of biomethane (<5 c€/kWh; < 3.5 gCO2-eq/MJ), Spirulina powder (<68 €/kg; < 4 kgCO2-eq/kg) and digestate (<5.60 €/tonne; < 0.41 kgCO2-eq/kg-nitrogen) are better than market-available alternatives across all scales. Trading emission savings from biomethane in the European Union emission trading system should allow the financial viability of smaller-scale processes by 2030.