Both the spatial distribution of leaves and leaf functions affect the light interception, transpiration and photosynthetic capacities of trees, but their relative contributions have rarely been investigated. We assessed these contributions at the branch and tree scales in two apple cultivars (Malus x domestica Borkh. 'Fuji' and 'Braeburn') with contrasting architectures, by estimating their branch and tree capacities and comparing them with outputs from a radiation absorption, transpiration and photosynthesis (RATP) functional-structural plant model (FSPM). The structures of three 8-year-old trees of each cultivar were digitized to obtain 3-D representations of foliage geometry. Within-tree foliage distribution was compared with shoot demography, number of leaves per shoot and mean individual leaf area. We estimated branch and tree light interception from silhouette to total leaf area ratios (STAR), transpiration from sap flux measurements and net photosynthetic rates by the branch bag method. Based on a set of parameters we previously established for both cultivars, the outputs of the RATP model were tested against STAR values, sap fluxes and photosynthetic measurements. The RATP model was then used to virtually switch foliage distribution or leaf functions (stomatal and photosynthetic properties), or both, between cultivars and to evaluate the effects on branch and tree light interception, transpiration and photosynthetic capacities in each cultivar. 'Fuji' trees had a higher proportion of leaf area borne on long shoots, fewer leaves per unit shoot length and a larger individual leaf area than 'Braeburn' trees. This resulted in a lower leaf area density and, consequently, a higher STAR in 'Fuji' than in 'Braeburn' at both branch and tree scales. Transpiration and photosynthetic rates were significantly higher in 'Fuji' than in 'Braeburn'. Branch heterogeneity was greater in 'Braeburn' than in 'Fuji'. An analysis of the virtual switches of foliage distribution or leaf function showed that differences in leaf spatial distribution and functions had additive effects that accounted for the lower transpiration and photosynthetic rates of branches and trees of 'Braeburn' compared with 'Fuji'. Leaf distribution had a more important role at the branch scale than at the tree scale, but the leaf function effect exceeded the leaf distribution effect at both scales. Our study demonstrated the potential of FSPM to disentangle physiological differences between cultivars through in silico scenarios.