Hydrochars obtained via hydrothermal carbonisation of pistachio shells are both a sustainable and an efficient alternative to commercial activated carbons for the removal of micro-pollutants from wastewaters that are difficult to handle by conventional treatments. Here a combined experimental and molecular simulation approach is adopted for the study of the caffeine/hydrochars aqueous systems. This case study serves to tune a general framework for the rational customisation of surface functional groups on hydrochars for the selective adsorption of micro-pollutants from wastewaters. Caffeine’s solubility, self-diffusion and adsorption results from aqueous solutions at relevant conditions are presented. Insights about the role of surface functional groups over the caffeine adsorption mechanism into hydrochars are gained and discussed.