The ability of species to adjust their light energy uptake is determined during plant establishment and development. Changes in resource availability may impact energy fluxes and photosynthesis. General and specific variations in chlorophyll a fluorescence under high vs. low water and nutrient conditions have been studied. N2-fixing leguminous trees, which are commonly used in tropical forest restoration, seem to be very well adapted to degraded ecosystems. To understand the effects of biological nitrogen fixation on Chl a fluorescence variables, three of the six Fabaceae species selected for this study were N2-fixing species. Additionally, the correlation among Chl a fluorescence and growth, photosynthesis and nutrient levels was evaluated. A 24-month forest restoration experiment was established, and data on dark-adapted Chl a fluorescence, photosynthesis, diameter growth and foliar nutrients were collected. Multivariate analysis was performed to detect the effects of seasonality and fertilization. Under high water- and nutrient-availability conditions, plants exhibited enhanced performance index values that were correlated with electron transport fluxes. Under drought and nutrient-poor conditions, most species exhibited increased energy dissipation as a method of photoprotection. Great interspecific variation was found; therefore, species-specific responses to the test conditions should be considered in future studies. N2-fixing species showed increased performance index and maximum fluorescence values, indicating their ability to colonize high-light environments. Negative correlations were found between photosynthesis and trapped fluxes and between diameter growth and initial fluorescence. Electron transport fluxes were positively correlated with growth. Given the different responses identified among species, Chl a fluorescence is considered a cost-effective technique to screen for seasonality, nutrient and N2-fixing species effects and should be considered for use during forest restoration. Finally, including N2-fixing species and multiple fertilization treatments in related studies may greatly facilitate the restoration of biogeochemical cycles in the tropics.