The present study aimed at determining whether mineral biofortified pearl millets will continue to maintain significantly higher iron and zinc contents after processing, and the effects of decortication, steeping/fermentation and parboiling on mineral, phytate and total phenolic contents in eight varieties of pearl millets (two biofortified hybrids, Dhanashakti and ICMH 1201, five improved varieties with high iron content and one traditional variety) were also investigated. The hybrids showed higher iron and zinc contents after processing compared to the improved varieties, for example, 17–51% and 10–26% higher iron and zinc contents, respectively, after steeping/fermentation followed by decortication compared to the best varieties. Phytate:mineral ratios also indicated that iron bioavailability was higher in the hybrids after processing, several times above the critical 1:1 ratio. Across all the types, iron content after processing was positively correlated (P ≤ 0.05) with high kernel weight, large kernels, and high fat content, and zinc content was positively correlated with high fat content. These kernel characteristics should aid in the selection of high iron and zinc pearl millet types.