A defining characteristic of superconductors is their tendency to expel magnetic fields, yet above a critical threshold, magnetic flux penetrates in discrete quanta carried by Abrikosov vortices1. The superconducting gap is completely suppressed at the vortex core, rendering them dissipative, semi-classical entities that impact applications from high-current-density wires to quantum devices. Material disorder can drive a crossover to vortices that preserve an energy gap at the core2–4, owing to intrinsic5 or emergent granularity on the scale of the coherence length2,6. Although quantum vortex behaviour could emerge in this effective tunnel-junction regime7, and signatures have been observed in diverse systems8–10, coherent manipulation of vortex states has remained elusive. Here we present evidence that vortices trapped in granular superconducting films can behave as two-level systems, exhibiting microsecond-range quantum coherence and energy relaxation times that reach fractions of a millisecond. Using the tools of circuit quantum electrodynamics11, we perform coherent manipulation and quantum non-demolition readout of vortex states in granular aluminium microwave resonators, heralding future directions for quantum information processing, materials characterization and sensing.
