Vacuolated spherical kafirin microparticles mean diameter 5 µm, can be formed from an acidic solution with water addition. Three dimensional scaffolds for hard tissue repair require large structures with a high degree of interconnected porosity. Cross-linking the formed kafirin microparticles using wet heat or glutaraldehyde treatment resulted in larger structures (approx. 20 µm), which whilst similar in size and external morphology, were apparently formed by further assisted-assembly by two significantly different mechanisms. Heat treatment, which increased vacuole size, involved kafirin polymerization by disulfide bonding with the microparticles being formed from round, coalesced nanostructures, as shown by AFM. Kafirin polymerization of glutaraldehyde treated microparticles was not by disulfide bonding and the nanostructures, as revealed by AFM, were spindle shaped. Both treatments enhanced BMP-2 binding to the microparticles, probably due to their increased size. Thus, these modified kafirin microparticles have potential as natural, non-animal protein bio-active scaffolds.