Extending the range of quantum interferometry to a wider class of composite nanoparticles requires new tools to diffract matter waves. Recently, pulsed photoionization light gratings have demonstrated their suitability for high mass matter-wave physics. Here, we extend quantum interference experiments to a new class of particles by introducing photofragmentation beam splitters into time-domain matter-wave interferometry. We present data that demonstrate this coherent beam splitting mechanism with clusters of hexafluorobenzene and we show single-photon depletion gratings based both on fragmentation and ionization for clusters of vanillin. We propose that photofragmentation gratings can act on a large set of van der Waals clusters and biomolecules which are thermally unstable and often resilient to single-photon ionization.