Microbial rhodopsins are a large family of photoreceptive membrane proteins with diverse light-regulated functions. While the most ubiquitous microbial rhodopsins are light-driven outward proton (H) pumps, new subfamilies of microbial rhodopsins transporting H inwardly, i.e., light-driven inward H pumps, have been discovered recently. Although structural and spectroscopic studies provide insights into their ion transport mechanisms, the minimum key element(s) that determine the direction of H transport have not yet been clarified. Here, we conducted the first functional conversion study by substituting key amino acids in a natural outward H-pumping rhodopsin (R) with those in inward H-pumping rhodopsins. Consequently, an artificial inward H pump was constructed by mutating only three residues of R. This result indicates that these residues govern the key processes that discriminate between outward and inward H pumps. Spectroscopic studies revealed the presence of an inward H-accepting residue in the H transport pathway and direct H uptake from the extracellular solvent. This finding of the simple element for determining H transport would provide a new basis for understanding the concept of ion transport not only by microbial rhodopsins but also by other ion-pumping proteins.