Abstract Oil refining sector contributes for 4% of the overall anthropogenic CO2 emissions and it is recognised as an important industrial sector for the implementation of carbon capture and storage technologies. This work focuses on the investigation of oil refinery emission sources and the specific development of a multi-energy SOFC-based system for the combined production of hydrogen, electricity and process steam with carbon capture. The system is sized to satisfy the fraction of refinery hydrogen demand, i.e., 22,500 Nm3 h−1 – conventionally covered by natural gas fired steam methane reformers. Four plant layouts are designed for this purpose featuring different levels of integration with the refinery process. The thermodynamic analysis shows the potentialities in terms of primary energy savings compared to separate production with conventional technologies. CO2 emissions can be reduced by 85% compared to reference cases, reaching zero or negative overall emissions due to the exported steam and electricity. A preliminary economic analysis is performed to establish the value of the levelised cost of hydrogen, to define its dependence on the carbon tax value and compare its value with difference hydrogen production technologies. This works shows the possibility of producing hydrogen at 3.3 € kg−1 in a current cost scenario.