The central role of the IW layers on plant leaves in controlling functions such as in restricting water loss and determining molecular diffusion rates to the leaf surface is well established and is important for both biological understanding and for developing agrochemical crop protection strategies. Directly observing and quantifying the heterogeneous 'brick and mortar' model, the hypothesized leaf wax structure, is therefore crucial for understanding the mechanisms underpinning its functions. Our nanoscale analyses of replicate leave waxes reveal the coexistence of highly ordered domains within larger grains within each crystal together with nematic phases of disordered chains surrounding the domains of lamellar packing. These observations refine the 'brick and mortar' with nanoscale crystallographic precision. Moreover, the systematic variation in nematic phase content, loss of lamellar domains, and reduction in grain microstructure with alcohol content, points to the balance of n-alkane and n-alkanol composition as a source of composition-determined microscopic diffusion pathways through the IW layer in plant leaves. The microscopic heterogeneity of these waxes provides the structural outlines for mechanistic models of layer flexibility and permeability (to water) in leaf waxes. Whilst we focus primarily on the application of this work to understanding the microstructural heterogeneity in leaf waxes these findings offer methods as well as structural features relevant for consideration in other related materials systems. Such systems include wax-tuned, lipid crystallization pathways in oil in water emulsions in food and pharmaceutical applications and pharmaceutically relevant formulations such as layered structures, e.g., in the form of coatings or layered nanoparticles , or formulations containing long chain polymer systems, e.g., solid dispersions , where product performance is based on interactions between multiple, distinct microscopic structures.