In our earlier works, we have identified rate-limiting steps in the dark-to-light transition of PSII. By measuring chlorophyll a fluorescence transients elicited by single-turnover saturating flashes (STSFs) we have shown that in diuron-treated samples an STSF generates only F1 (< Fm) fluorescence level, and to produce the maximum (Fm) level, additional excitations are required, which, however, can only be effective if sufficiently long Δτ waiting times are allowed between the excitations. Biological variations in the half-rise time (Δτ1/2) of the fluorescence increment suggest that it may be sensitive to the physicochemical environment of PSII. Here, we investigated the influence of the lipidic environment on Δτ1/2 of PSII core complexes of Thermosynechococcus vulcanus. We found that while non-native lipids had no noticeable effects, thylakoid membrane lipids considerably shortened the Δτ1/2, from ~ 1 ms to ~ 0.2 ms. The importance of the presence of native lipids was confirmed by obtaining similarly short Δτ1/2 values in the whole T. vulcanus cells and isolated pea thylakoid membranes. Minor, lipid-dependent reorganizations were also observed by steady-state and time-resolved spectroscopic measurements. These data show that the processes beyond the dark-to-light transition of PSII depend significantly on the lipid matrix of the reaction center.