Hydrogen is expected to play a significant role as a clean energy carrier. However, the development of a hydrogen economy requires the use of large amounts of hydrogen; therefore, large-scale hydrogen storage is a considerable problem that needs to be resolved. Hydrogen can be stored underground in aquifers, salt caverns, depleted oil and gas reservoirs, and coal seams. In this context, wettability is a critical parameter in determining the containment security, storage capacity, fluid dynamics, and withdrawal rate during underground hydrogen geo-storage operations. Meanwhile, the toxic soluble dye, methyl orange (MO), is widely used in the textile and other industries and released in large quantities into the surface and subsurface waters. Hence, in the present study, the use of MO to alter the wettability of reservoirs in favor of hydrogen geo-storage is investigated. To this end, model oil-wet rock surfaces are prepared by aging quartz substrates with stearic acid and then treating them with various amounts of aqueous MO for 1 week at 50 °C. The brine contact angles on these model surfaces are then measured in a hydrogen environment under various reservoir conditions to demonstrate that the MO treatment makes the surface more hydrophilic. Moreover, the contact angle is seen to increase significantly with the increase in the temperature, pressure, and salinity. In addition, the importance of pH is assessed, and various brines (NaCl, KCl, MgCl2, and CaCl2) are compared. The proposed treatment is expected to improve the hydrogen trapping efficiency of sandstone reservoirs while simultaneously providing a safe disposal route for MO via deep well injection.