This study provides a novel approach to encounter the well-established global issues of drug-resistant pathogens bacterial/fungal strains and their linked metabolites such as aflatoxins (AFs). Recent advancements have been proposed for incorporation nanoparticles (NPs) in this regards. This study provides a promising solution to control pathogenic moulds and AFs by the utilization of nanotechnology approach and also highlighted the AFs level in various agricultural commodities. A variety of agricultural commodities such as wheat, composite spices and dry fruits/edible nuts were assessed for the AFs determination by HPLC. The iron (Fe), copper (Cu) and silver (Ag) NPs have been synthesized from bio-diversified plants, herbs and spices extracts and chemical reduction method in parallel. These great varieties of NPs are used to control AFs and pathogenic moulds. AFs were detected in 26−77% of samples; the average concentration was found 0.53−4.63 µg/kg with contamination ranged of 0.02−30.11 µg/kg. The spherical shape NPs were successfully synthesized with average particle size ranges from 10−120 nm. Ag-NPs showed a pronounced effect, thereby reducing the growth of methicillin- and vancomycin-resistance Staphylococcus aureus at MIC of 8−16, 32−64 and 128−256 µg/mL for Ag-, Cu- and Fe-NPs, respectively. The growth of aflatoxigenic moulds (Aspergillus) and AFs production was significantly inhibited in presence of 100 µg/mL Ag-NPs, in contrast to Fe- and Cu-NPs. The batch adsorption test for the efficacy of NPs to adsorb aflatoxin B1 (AFB1) indicates that ≥ 95% AFB1 adsorption using 5 mg/mL NPs. Adsorption data was well fitted in Langmuir isotherm model with different adsorption capacities. Kinetics and thermodynamic studies indicates spontaneous adsorption process that is endothermic in nature and follows the pseudo-second order rate equation. The efficiencies of green synthesized NPs were found in the order of: green tea > black tea > clove > neem > datura > jamun > curry leaves > rose > black cumin > mangroves > gum tree > dates. The synthesis of metal NPs using green nanotechnology seems to be the best candidate because it is simple, eco-friendly, costeffective, non-toxic, energy-efficient and considered as alternative to the conventional methods. This study explores the importance of green chemistry, thereby demonstrating for the first time, the successful utilization of green nano synthesis approach for the control of AFs and pathogenic moulds. The NPs could be utilized as alternative antimicrobial agents in medical, agricultural and veterinary fields.