Tailoring chemical composition is the primary route to achieving desired properties of materials, including technologically important ABO₃-type perovskite oxides. This approach is generally assumed to translate directly to thin films. In contrast, this study demonstrates that substrates can significantly modify compositional effects in thin films. Specifically, transition-metal (M = Mn, Fe, Co, Ni) substitution is experimentally investigated in thin films of the archetypal perovskite SrTiO₃ grown by pulsed laser deposition on different substrates. It is found that substrate-induced lattice strain regulates the preferential sites for M substitution and leads to an increase in the direct optical bandgap. In the absence of strain, doping with M cations has no effect on the bandgaps. Substrate-imposed strain and/or substitution are found to induce band tailing and weak sub-gap optical absorption. These findings highlight the unique role of substrates in engineering the chemical composition and functional properties of thin films.