In fossil-based refinery and biorefinery applications hydrogen is recovered by pressure swing adsorption and subsequently re-pressurized using mechanical compressors. Electrochemical hydrogen compression is an efficient way of separating and compressing H2 from a gaseous mixture within a compact device. In this work, a preliminary investigation of the integration of a bio-oil hydroprocessing unit with a complete novel gas polishing and separation unit was conducted. Apart from the electrochemical compressor, this includes a CO methanation reactor and a ZnO bed to remove the contained CO and H2S impurities of the hydroprocessing reactor outlet and safeguard the trouble-free operation of the electrochemical device. This first assessment revealed that several operating parameters such as the hydrotreating pressure, the gas polishing and separation temperature and the hydrogen recycling ratio limit the possible operating modes of the subsequent units.