The classical theory of the relationship between gas fluxes and photosynthetic electron fluxes was extended by two additional terms: JL describing flux to electron sinks other than the Calvin cycle, and RL accounting for light-induced changes in non-photorespiratory CO2 evolution. RL comprises two main components, Rr resulting from light-induced decrease in tricarboxylic acid activity, and RS related to extra CO2 evolution resulting from citrate-to-2-oxoglutarate conversion for N-assimilation in NO3– grown leaves. This extended theory was applied to two experiments. First, A–Ci curves (dependence of CO2 flux on stomatal CO2 concentration) revealed a higher apparent CO2 compensation point (Γ*app) in NO3–-grown plants than in NH4+-grown plants. Secondly, photosynthetic electron fluxes at different light intensities were determined by means of the Genty parameter of chlorophyll fluorescence and compared with those calculated from measured CO2 uptake. Curve-fitting based on the extended theory provided a coincidence of these two measurements and resulted in higher RS in NO3–-grown than in NH4+-grown plants. This difference in RS (about 15% of the CO2 flux bound by carboxylation) is the same as that obtained from the analysis of Γ*app. Further, the analysis suggests that JL related to the extra electron flux used for N-assimilation in NO3–-grown plants is diverted to other sinks in NH4+-grown plants. SHAM decreased photosynthetic electron flow and O2 evolution in NH4+-grown plants, antimycin A in NO3–-grown plants. The effect of oligomycin was small. The results are discussed in terms of different mechanisms of chloroplast/mitochondrion interaction in NO3–- and NH4+-grown plants, their effects on non-photorespiratory CO2 evolution and on Γ*app.