Coherent photon-emitter interfaces offer a way to mediate efficient nonlinear photon-photon interactions, much needed for quantum information processing. Here we experimentally study the case of a two-level emitter, a quantum dot, coupled to a single optical mode in a nanophotonic waveguide. We carry out few-photon transport experiments and record the statistics of the light to reconstruct the scattering matrix elements of one- and two-photon components. This provides direct insight to the complex nonlinear photon interaction that contains rich many-body physics.