Phosphate and sulfate groups play an important role in controlling the physical properties of biomolecules and artificial materials. However, despite their significance, the incorporation of phosphate or sulfate groups into aqueous organic compounds using non-enzymatic methods has been unprecedented. In this study, we have successfully conjugated inorganic phosphate and sulfate with aminocyclobutenedione derivatives via photochemical reactions under aqueous conditions. A plausible mechanism for the conjugation reactions was proposed on the basis of DFT calculations. These reactions will promote life science research based on organophosphates and organosulfates which have been difficult to access up to now.