The controlled integration of magnetic molecules into superconducting circuits is key to developing hybrid quantum devices. Herein, we study [Dy2] molecular dimers deposited into micro-SQUID susceptometers. The results of magnetic, heat capacity and magnetic resonance experiments, backed by theoretical calculations, show that each [Dy2] dimer fulfills the main requisites to encode a two-spin quantum processor. Arrays of between 2 × 108 and 7 × 109[Dy2] molecules were optimally integrated under ambient conditions inside the 20 μm wide loops of micro-SQUID sensors by means of dip-pen nanolithography. Equilibrium magnetic susceptibility and phonon-assisted spin tunneling dynamics measured in situ substantiate that these molecules preserve spin ground states, magnetic interactions and magnetic asymmetry that characterize them in bulk. These results show that it is possible to interface multi-qubit molecular complexes with on-chip superconducting circuits without disturbing their relevant properties and suggest the potential of soft nanolithography techniques to achieve this goal.