Imperfect photons’ indistinguishability limits the performance of photonic quantum communication and computation . Distillation protocols, inspired by entanglement purification, enhance photons’ indistinguishability by leveraging quantum interference in linear optical circuits. In this work, we present a three-photon distillation protocol optimized to achieve the maximum visibility gain, which requires consideration of multi-photon effects such as collective photonic phases. We employ interferometers with the minimum number of modes, optimizing also over the protocol’s success probability. The developed protocol is experimentally validated with a platform featuring a demultiplexed quantum dot source interfaced with a programmable eight-mode laser-written integrated photonic processor. We achieve indistinguishability distillation with limited photonic resources and for several multi-photon distinguishability scenarios. This work helps to strengthen the role of distillation as a practical tool for photon-based quantum technologies.