The aim of the present study was to characterize the probiotic qualities of Bacillus isolates and study their siderophore prior to possible siderophoregenic probiotic application for iron nutrition in animals and humans. Bacillus strains were selectively isolated from dairy waste and mango pulp waste. Best two siderophore positive isolates, JHT3 and DET6 showed high homology with Bacillus megaterium (98%) and B. subtilis (99%), respectively, using partial 16S-rRNA sequencing and biochemical characterization. These isolates produced catecholate type of siderophore under iron stressed conditions and were screened for probiotic properties as per WHO and FAO guidelines. Spores of these strains showed excellent tolerance in partially simulated gastrointestinal tract conditions and exhibited antimicrobial activity against organisms such as Staphylococcus aureus, Micrococcus flavus and Escherichia coli. Importantly, these isolates were susceptible to the most of the antibiotics tested, in conflict that they would not donate resistance determinants if administered in the form of probiotic preparations.