Rhodopsins hosting synthetic retinal protonated Schiff base analogues are important for developing tools for optogenetics and high-resolution imaging. The ideal spectroscopic properties of such analogues include long-wavelength absorption/emission and fast/hindered photoisomerization. While the former may be achieved, for instance, by elongating the chromophore π-system, the latter requires a detailed understanding of the substituent effects (i.e., steric or electronic) on the chromophore light-induced dynamics. In the present letter we compare the results of quantum mechanics/molecular mechanics excited-state trajectories of native and analogue-hosting microbial rhodopsins from the eubacterium Anabaena. The results uncover a relationship between the nature of the substituent on the analogue (i.e., electron-donating (a Me group) or electron-withdrawing (a CF3 group)) and rhodopsin excited-state lifetime. Most importantly, we show that electron-donating or -withdrawing substituents cause a decrease or an increase in the electronic mixing of the first two excited states which, in turn, controls the photoisomerization speed.