Perovskite solar cells and light-emission devices are yet to achieve their full potential owing in part to microscale inhomogeneities and defects that act as non-radiative loss pathways. These sites have been revealed using local photoluminescence mapping techniques but the short absorption depth of photons with energies above the bandgap means that conventional one-photon excitation primarily probes the surface recombination. Here, we use two-photon time-resolved confocal photoluminescence microscopy to explore the surface and bulk recombination properties of methylammonium lead halide perovskite structures. By acquiring 2D maps at different depths, we form 3D photoluminescence tomography images to visualise the charge carrier recombination kinetics. The technique unveils buried recombination pathways in both thin film and micro-crystal structures that aren’t captured in conventional one-photon mapping experiments. Specifically, we reveal that light-induced passivation approaches are primarily surface-sensitive and that nominal single crystals still contain heterogeneous defects that impact charge-carrier recombination. Our work opens a new route to sensitively probe defects and associated non-radiative processes in perovskites, highlighting additional loss pathways in these materials that will need to be addressed through improved sample processing or passivation treatments.