Knowledge about the dynamical properties of a protein is of essential importance for understanding the structure–dynamics–function relationship at the atomic level. So far, however, the correlation between internal protein dynamics and functionality has only been studied indirectly in steady-state experiments by variation of external parameters like temperature and hydration. In the present study we describe a novel type of (laser-neutron) pump-probe experiment, which combines in situ optical activation of the biological function of a membrane protein with a time-dependent monitoring of the protein dynamics using quasielastic neutron scattering. As a first successful application we present data obtained selectively in the ground state and in the M-intermediate of bacteriorhodopsin (BR). Temporary alterations in both localized reorientational protein motions and harmonic vibrational dynamics have been observed during the photocycle of BR. This observation is a direct proof for the functional significance of protein structural flexibility, which is correlated with the large-scale structural changes in the protein structure occurring during the M-intermediate. We anticipate that functionally important modulations of protein dynamics as observed here are of relevance for most other proteins exhibiting conformational transitions in the time course of functional operation.