Mitigating the effects of changing climate with adaptable cultivars while reducing the input burden of additional selection criteria is becoming a priority, especially as water shortage is limiting soybean production in Europe. To evaluate the functionality of the photosynthetic apparatus in drought, chlorophyll a (Chl a) fluorescence was measured in 16 elite soybean lines in drought and conditions with sufficient water supply in V2 (second node), R1 (beginning bloom), R4 (full pod), R5 (beginning seed) and R6 (full seed) stages. Developmental stage was a significant source of variation for all parameters, and PI total was chosen as the most sensitive parameter in detecting the average drought effect. Genotypes G5, G9, and G10 had superior overall functioning of the photosynthetic apparatus in drought, while the photosynthetic apparatus of G12 and G16 was the least functional. The drought effect was determined to be the most relevant in R1, R4 and R6. G14 had highest PI total in drought conditions in R1 and R4, while G9 had the highest drought-stressed PI total in R6. G7 had the lowest drought-stressed PI total in R1, G4 and G6 had the lowest in R4, and G8 had the lowest in R6. PI total proved useful in breeding for abiotic stress tolerance, especially for excluding the material with the poorest photosynthetic apparatus function, which increases the efficiency of the selection process when a large number of genotypes needs to be screened. However, genotypes with superior photosynthetic apparatus functioning should be further tested in yield trials to confirm their drought tolerance and value for use in drought conditions.