Background: Cyperus esculentus L. is a herbaceous plant which grows well in Northern Nigeria and other parts of the world. The rhizomes among other uses are used to process an artisanal beverage called ‘kunun-aya’ in Northern Nigeria while the leaves have other medicinal uses. Objective: This study was aimed at assessing the chitosan nanoparticles treatment approach for artisanal ‘kunun-aya’ beverages sold in some Northern Nigeria markets against resistance microorganisms found in the drink. Method: Phytochemical contents, metallic elements, and physicochemical analysis of the rhizome extract were assessed following standard procedures. The artisanal ‘kunun-aya’ beverage was prepared by fermentation process following local methods of preparation in large basin. The preparation of chitosan nanoparticles was carried out using nano spray drying technique while microbial analysis and susceptibility testing were carried out using standard methods. Results: The results showed that there are Escherichia coli, coliform bacteria, Bacillus spp., Aspergillus sp., Penicillium spp., Streptococcus spp., Salmonella-Shigella and Staphylococcus aureus in all the artisanal kunun-aya beverages obtained from all the local markets. The presence of these microorganisms was prevalent in those obtained from the Kano, Bauchi and Sokoto markets while those obtained from the Jos markets were the lowest. The study did not show heavy presence of heavy metals such as cadmium, arsenic and lead. The study further showed that kunun-aya beverage mediately prepared using chitosan nanoparticles did not show any microbial growth on culture media after 48 hours. Similarly, there was no presence of either heavy or trace metals when the sample was analyzed using atomic absorption spectrophotometry. Finally, there were no significant differences (p < 0.05) among the artisanal kunun-aya beverages from various northern Nigeria markets. Conclusion: The study, therefore, showed that chitosan nanoparticles-mediated treatment for kunun-aya (Cyperus esculentus) beverages is a promising treatment strategy against microorganisms found in artisanal kunun-aya local beverages sold in northern Nigeria.