Characterization and quantum control of complex quantum matter is one of the shared goals for condensed matter and quantum information science research. Toward this end, my research uses van der Waals materials to synthesize topological and correlated states, and quantum sensors based on spin defects to uncover their microscopic picture. Focusing on superconductivity as the theme of this talk, I will first present pathways to program the electron correlation in moiré graphene by exploiting the lattice degree of freedom, both in the planar and vertical directions. In the second part, I will show new experimental observables, unlocked by the nanoscale magnetometer based on the nitrogen vacancy center in diamond, can uncover hidden physics. As an example, quantitative visualization of the super current flow in a SNS Josephson junction is used to reveal electrically configurable ground states in the zero-resistance regime. A surprising role of the kinetic inductance and the implications for the Josephson diode effect will be discussed. Finally, I will share my vision to integrate programmable quantum materials with nanoscale quantum sensors.