We unveil the signature of many-body interference across dynamical regimes of the Bose-Hubbard model. Increasing the particles' indistinguishability enhances the temporal fluctuations of few-body observables, with a dramatic amplification at the onset of quantum chaos. By resolving the exchange symmetries of partially distinguishable particles, we explain this amplification as the fingerprint of the initial state's coherences in the eigenbasis.