The Germplasm Bank of Stevia rebaudiana segregants of the University of Córdoba is a strategy for the use of genetic variability and efficient crop yield. There are genotypes with important characteristics such as: high tolerance to salt stress and climatic change (high CO2 in the Earth surface), late flowering, erect architecture, and high contents of steviol glycosides. However, there is a lack of in-depth studies of morphophysiological and biochemical indicators such as gas exchange, chlorophyll a fluorescence, chloroplast pigments, and antioxidant systems, which allow us to develop early selection tools for elite genotypes. The genotypes (L020, Morita II, and L102) were found to have elite characteristics such as high efficiency in water use, excellent biomass production, and a more robust antioxidant system than the genotypes (L057 and L082). The L020 genotype presented the highest content of stevioside and rebaudioside A, followed by the Morita II genotype. We found a close correlation between the electron transport rate and the mechanisms that increase photosystem complexes. In this sense, non-photochemical cooling modulated by the release of heat by the leaves is a fact that is confirmed by the greater activity of the xanthine pool to protect the photochemical complexes in S. rebaudiana.