Phonons and their interactions with other phonons, electrons or photons drive energy gain, loss and transport in materials. Although the phonon density of states has been measured and calculated in bulk crystalline semiconductors, phonons remain poorly understood in nanomaterials, despite the increasing prevalence of bottom-up fabrication of semiconductors from nanomaterials and the integration of nanometre-sized components into devices. Here we quantify the phononic properties of bottom-up fabricated semiconductors as a function of crystallite size using inelastic neutron scattering measurements and ab initio molecular dynamics simulations. We show that, unlike in microcrystalline semiconductors, the phonon modes of semiconductors with nanocrystalline domains exhibit both reduced symmetry and low energy owing to mechanical softness at the surface of those domains. These properties become important when phonons couple to electrons in semiconductor devices. Although it was initially believed that the coupling between electrons and phonons is suppressed in nanocrystalline materials owing to the scarcity of electronic states and their large energy separation, it has since been shown that the electron-phonon coupling is large and allows high energy-dissipation rates exceeding one electronvolt per picosecond (refs 10-13). Despite detailed investigations into the role of phonons in exciton dynamics, leading to a variety of suggestions as to the origins of these fast transition rates and including attempts to numerically calculate them, fundamental questions surrounding electron-phonon interactions in nanomaterials remain unresolved. By combining the microscopic and thermodynamic theories of phonons and our findings on the phononic properties of nanomaterials, we are able to explain and then experimentally confirm the strong electron-phonon coupling and fast multi-phonon transition rates of charge carriers to trap states. This improved understanding of phonon processes permits the rational selection of nanomaterials, their surface treatments, and the design of devices incorporating them.