We investigate, with a combination of ultrafast optical spectroscopy and semiclassical modeling, the photothermal properties of various water-soluble nanocrystal assemblies. Broadband pump–probe experiments with ∼100-fs time resolution in the visible and near infrared reveal a complex scenario for their transient optical response that is dictated by their hybrid composition at the nanoscale, comprising metallic (Au) or semiconducting (Fe3O4) nanostructures and a matrix of organic ligands. We track the whole chain of energy flow that starts from light absorption by the individual nanocrystals and subsequent excitation of out-of-equilibrium carriers followed by the electron–phonon equilibration, occurring in a few picoseconds, and then by the heat release to the matrix on the 100-ps timescale. Two-dimensional finite-element method electromagnetic simulations of the composite nanostructure and multitemperature modeling of the energy flow dynamics enable us to identify the key mechanism presiding over the light–heat conversion in these kinds of nanomaterials. We demonstrate that hybrid (organic–inorganic) nanocrystal assemblies can operate as efficient nanoheaters by exploiting the high absorption from the individual nanocrystals, enabled by the dilution of the inorganic phase that is followed by a relatively fast heating of the embedding organic matrix, occurring on the 100-ps timescale.