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Evaluating residual lead (Pb) and cadmium (Cd) levels in food products, especially milk, is critical for product safety and quality. In this purview, the current study aims to determine Pb and Cd concentrations in milk using atomic absorption spectrophotometry and compare their values with international standards. In addition, it aims to remove these metals from milk samples using low-cost, naturally occurring materials, such as bentonite, date pit, and chitosan nanoparticles. The ability of potential adsorbents was also investigated using Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), and transmission electron microscope (TEM). Moreover, their impact on milk’s nutritional properties was considered. The results revealed that most milk samples contained Pb and Cd, with mean values of 0.237 ± 0.179 and 0.041 ± 0.036 mg/kg, respectively. Furthermore, the three possible adsorbents demonstrated high sequestering ability due to their existing functional groups; the adsorption capacity of bentonite to Pb and Cd was 84 and 88%, date pit was 97 and 93%, and chitosan nanoparticles were 82 and 98%, respectively, with no discernible change in milk nutritional contents. In conclusion, the bentonite, date pit, and chitosan nanoparticles were found to be significantly effective and safe in removing hazardous trace elements (Pb and Cd) from contaminated milk. Graphical abstract