SrTiO3 (STO) is often used as a substrate for growing thin superconducting films. STO undergoes a structural transition at 105K, where the lattice breaks into tetragonal domains. We use a scanning Superconducting Quantum Interference Device (SQUID) to map the diamagnetic response of Nb and NbN deposited on STO, at their SC phase. We show that STO domains and domain walls cause large scale modulations of the superfluid density, opening possibility for better understanding of the effect of local structure on superconductivity, and a local control of the strength of superconductivity.