It is demonstrated that a transition metal redox-active ion can exhibit amphoteric dopant substitution in the SrTiO3 perovskite lattice. In stoichiometric SrTiO3, the manganese dopant is preferably accommodated through isovalent substitution as Mn2+ on the strontium site and as Mn4+ on the titanium site. Previous studies have suggested that either type of substitution is possible for compositions with tailored Sr/Ti stoichiometry. Using electron paramagnetic resonance (EPR) spectroscopy, the site occupancy of dilute concentrations of manganese is investigated in SrTiO3 as a function of the Sr/Ti ratio. The tuned Sr/Ti ratio can be used to manipulate the nature of the manganese substitution, and it is shown that Sr-rich compositions (Sr/Ti > 1.001) processed in air result in B-site isovalent doping. For B-site substituted manganese ions, a new EPR signal for aliovalent Mn2+ is observed in compositions annealed under reducing atmosphere. The concentration of oxygen vacancies observed with EPR is also shown to depend on the Sr/Ti stoichiometry. With improved control over the site of substitution and valence state, doping with a transition metal redox-active ion may facilitate the ability to engineer new electronic functionality into the perovskite lattice.