The ability to implement reconfigurable linear optical circuits is a fundamental building block for the implementation of scalable quantum technologies. Here, we implement such circuits in a multimode fiber by harnessing its complex mixing using wavefront shaping techniques. We program linear transformations involving spatial and polarization modes of the fiber and experimentally demonstrate their accuracy and robustness using two-photon quantum states. In particular, we illustrate the reconfigurability of our platform by emulating a tunable coherent absorption experiment, where output probabilities of single-and two-photon survivals can be controlled. By demonstrating complex, reprogrammable, reliable, linear transformations, with the potential to scale, our results highlight the potential of complex media driven by wavefront shaping for quantum information processing.