In the present study, we investigated the epoxidation reaction of the violaxanthin (Vx) cycle in intact cells of Chlorella vulgaris. Our results show that the overall epoxidation is slightly slower in darkness compared to the epoxidation during high light (HL) illumination. The calculation of the rate constants of the two epoxidation steps revealed that, for both conditions, the first epoxidation step from zeaxanthin (Zx) to antheraxanthin (Ax) is faster than the second epoxidation step from Ax to Vx. However, the most noteworthy result of our present study is that Ax, which is transiently formed during the epoxidation reaction, participates in non-photochemical quenching of chlorophyll fluorescence (NPQ). A correlation between NPQ and the de-epoxidized xanthophyll cycle pigments during the time-course of the epoxidation reaction can only be achieved when NPQ is plotted versus the sum of Zx and Ax. The accumulation of significant amounts of Ax during the epoxidation reaction further indicates that Ax-dependent quenching proceeds with a similar efficiency compared to the Zx-mediated NPQ. As the xanthophyll-dependent NPQ relies on the presence of de-epoxidized xanthophylls in the PS II antenna, Ax-dependent NPQ is only possible under the assumption that Ax rebinds to the light-harvesting complex (LHC) II during the epoxidation reaction.