BACKGROUND: Part I introduced the concept of easy- and difficult-to-mill chickpea genotypes, the broad chemical composition of their seed fractions and proposed mechanistic explanations for physical differences consistent with observed variation in milling ease. Part II continues this research by delving deeper into the amino acid, fatty acid and mineral components. RESULTS: No association between fatty acid composition and ease of milling was observed. However, particular amino acids and mineral elements were identified that further support roles of lectins, pectins and mineral-facilitated binding in the adhesion of chickpea seed coat and cotyledons. CONCLUSION: These differences suggest underlying mechanisms that could be exploited by breeding programmes to improve milling performance. This study shows that the content and composition of amino acids, fatty acids and minerals within different chickpea tissues vary with seed type (desi and kabuli) and within desi genotypes in ways that are consistent with physical explanations of how seed structure and properties relate to milling behaviour.