Hydrogen geo-storage could be the large-scale solution needed for a hydrogen economy. Biological factors have been considered but mainly in terms of hydrogen-metabolising microbes. We demonstrate consistently the direct influence of underground biofilm formation on the wettability of sandstone reservoirs. The biofilm, formed by incubation with cyanobacteria Geitlerinema sp. in seawater, increases the advancing and receding brine contact angles on water-wet quartz. The angles decrease only slightly on oil-wet quartz surfaces even though biomass accumulation is more significant. We formulate an explanation using Cassie's approach to heterogeneous surfaces, taking into account the predominant surface chemical groups. Wettability strongly affects the distribution, trapping and mobility of phases (brine and hydrogen) inside the rock formation. Our results, obtained at typical reservoir conditions (25–50 °C, 3–130 bar), are relevant to understanding and assessing hydrogen injectivity, withdrawal rates, storage capacity and containment security. This fundamental research supports the development of an industrial-scale decarbonized hydrogen economy.