Mother’s milk is a unique biological fluid providing essential nutrients for the proper growth and development of neonates. Surveillance reports indicated continuous exposure to various contaminants to humans. These xenobiotics tend to mobilize into multiple body fluids, including mother’s milk, thus creating a higher risk to mother’s milk-fed neonates. This study aimed to determine the extent of mycotoxins, trace and toxic metals contamination in mother’s milk, and health risk assessment of mother’s milk-dependent neonates. In this study, mycotoxins and metals were analyzed in the milk of 100 Indian nursing mothers. Aflatoxin M1(AFM1) was detected by ELISA, whereas Ochratoxin (OTA), α-Zearalenol(α-ZEL), β-Zearalenol (β-ZEL) and Zearalenone (ZEN) were analyzed by LC-HRMS. Metals were analyzed using ICP-MS. In the 100 analyzed samples, the detection of AFM1, OTA, ZEN, α-ZEL, and β-ZEL were 73%, 96%, 30%, 15%, and 7%, respectively. In breastfed infants, the estimated daily intake (EDI) of AFM1, OTA, and ZEN were 0.005, 0 0.047, and 0.024 µg/L BW/day. Similarly, metals analysis showed the presence of Cr, Mn, As, Cd, and Pb were 26%, 49%, 42%, 34%, and 12%, respectively. The HQ > 1 in arsenic indicates possible health risks for the infants. A significant correlation was found among all metals except As. α-ZEL, β-ZEL, and ZEN were significant among themselves. Altogether, results suggest a potential risk of mycotoxins and trace toxic metals for neonates via mother’s milk which requires immediate attention and must be regulated promptly.