The aim of this work was to compare gas exchanges from leaf to whole plant scales, in two Ethiopian accessions (‘E083’ and ‘E027’), and two bred cultivars (Iapar 59 and Catuaí 99) of Arabica coffee (Coffea arabica L.) cultivated under irrigated and rainfed conditions. Variations in gas exchanges were evaluated over four phenophases (leaf expansion – BE1 and BE2, and berry harvesting – BH1 and BH2), covering the first two production years in the coffee life cycle. We addressed the following questions: Are gas exchanges modified by water availability at leaf and/or plant scales? Do bred cultivars and wild accessions differ in their physiological responses to water availability and phenophases? Photosynthesis (A), stomatal conductance (gs), and transpiration (E) were measured on the recently fully expanded leaves at the upper canopy stratum. The functional-structural plant modelling (FSPM) was used to integrate A at whole plant photosynthesis (A”p), based on 3D virtual trees constructed under VPlants modelling platform. Despite high A values of ‘E083’ overall phenophases, a strong decline in A”p under rainfed condition was observed due to lower plant leaf area as compared to irrigated condition. Catuaí 99 and ‘E083’ were more sensitive to drought than Iapar 59 and ‘E027’, considering photosynthesis at leaf and plant scales. At the last BH2 phenophase, A, gs, E, and carboxylation efficiency were similar between irrigated and rainfed conditions for all genotypes, suggesting some acclimation of leaf gas exchange to the environment. However, A”p benefited by water management in all phenophases as plant leaf area increased. These findings revealed the need to develop methodologies for structural and functional analyses at plant scale, an important step towards the realistic responses of plants and orchards to the surrounding environment.