The intriguing mathematical properties of leaf phyllotaxis still attract scientific attention after centuries of research. Phyllotaxis, and in particular the divergence angle between successive leaves, have been frequently interpreted in terms of maximization of light capture, although certain model simulations of light capture by vertical shoots revealed minor effects of phyllotaxis in comparison with the effect of other morphological features of the plant. However, these simulations assumed a number of simplifications, did not take into account diffuse light, and were not based on real plants with their natural range of morphological variation. This study was aimed at filling these gaps by examining the influence on light harvesting of shoot architecture and divergence angle in four species with spiral phyllotaxis (Quercus ilex, Arbutus unedo, Heteromeles arbutifolia and Daphne gnidium) with a realistic 3-D model (Y-plant). A wide range of divergence angles (from 100° to 154°) was observed within each species, with 144° being the most frequent one. These different divergence angles rendered very different vertical projections of the shoot due to contrasting patterns of leaf overlap as seen from above, but they rendered indistinguishable light interception efficiencies (Ea). Setting the leaves with an opposite-decussate phyllotaxis led, however, to a 40–50% decrease of Ea. The interplay of internode length, leaf size and shape, and leaf elevation angle led to significant species differences in Ea. Thus, only particular phyllotaxis (e.g., decussate) might be functionally inefficient under certain combinations of the various morphological variables that influence light capture of a shoot.