A significant proportion of the global population is currently suffering from protein and mineral malnutrition. Food enrichment or fortification is an effective strategy being utilized worldwide to fight malnutrition. The objective of the study was to extract protein and minerals from an underutilized natural source of jackfruit seed and to incorporate these nutrients into a widely consumed food yogurt. Protein isolation was achieved through the removal of the major component starch from jackfruit seed flour (JSF) followed by spray drying to get jackfruit seed protein isolate (JSPI). Mineral extraction was performed from the residuals after protein extraction. Four different yogurt samples were formulated enriched with varying concentrations of extracted protein (8%, 6%, 4%, and 2%) and a constant mineral concentration of 747 mg/100 g of yogurt. A plain yogurt served as the control sample (S5), which was not enriched with protein and mineral. The yogurts were successfully enriched with protein and minerals in this study. The sensory evaluation experiment suggested that the yogurt sample (S2) prepared with 6% protein and 747 mg/100 g mineral secured better sensory acceptance than any other sample prepared in this study. Shelf-life study showed that the yogurts were safe for consumption up to 12 days when stored under refrigeration temperature and 4 days when stored at room temperature.