Strontium titanate SrTiO3 (STO) is a canonical example of a quantum paraelectric, and its doping with manganese ions unlocks its potential as a quantum multiferroic candidate. However, to date, the specifics of incorporation of the manganese ion into the perovskite lattice and its impact on structure-property relationships are debatable questions. Herein, using high-precision X-ray diffraction of a Mn (2 atom %)-doped STO single crystal, clear fingerprints of the displacement disorder of Mn cations in the perovskite B-sublattice are observed. Moreover, near the temperature of the antiferrodistortive transition, the off-center Mn position splits in two, providing the unequal potential barrier's distribution for possible local atomic hopping. A link with this was found via analysis of the dielectric response that reveals two Arrhenius-type relaxation processes with similar activation energies (35 and 43 meV) and attempt frequencies (1 × 1011 and ∼1.6 × 1010 Hz), suggesting similar dielectric relaxation mechanisms.