Quantum confinement can dramatically slow down electron-phonon relaxation in nanoclusters. Known as the phonon bottleneck, the effect remains elusive. Using a state-of-the-art time-domain ab initio approach, we model the observed bottleneck in CdSe quantum dots and show that it occurs under quantum Zeno conditions. Decoherence in the electronic subsystem, induced by elastic electron-phonon scattering, should be significantly faster than inelastic scattering. Achieved with multiphonon relaxation, the phonon bottleneck is broken by Auger processes and structural defects, rationalizing experimental difficulties.