Reconfigurable quantum circuits are fundamental building blocks for the implementation of scalable quantum technologies. Their implementation has been pursued in linear optics through the engineering of sophisticated interferometers. While such optical networks have been successful in demonstrating the control of small-scale quantum circuits, scaling up to larger dimensions poses significant challenges. Here, we demonstrate a potentially scalable route towards reconfigurable optical networks based on the use of a multimode fibre and advanced wavefront-shaping techniques. We program networks involving spatial and polarisation modes of the fibre and experimentally validate the accuracy and robustness of our approach using two-photon quantum states. In particular, we illustrate the reconfigurability of our platform by emulating a tunable coherent absorption experiment. By demonstrating reliable reprogrammable linear transformations, with the prospect to scale, our results highlight the potential of complex media driven by wavefront shaping for quantum information processing.