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Carrot (Daucus carota) is a root vegetable of Apiaceae family. Globally, the consumption of carrots tremendously increased due to their beneficial effects on human wellbeing. Increasing the shelf life of carrot is thus important and the enhanced qualities (mechanical resistance, diffusivity, optical properties, and solubility) of zinc oxide nanoparticles formulated through the synergistic action with Phyllanthus niruri have been found to exhibit antimicrobial and antioxidant qualities. The research was aimed at extending the shelf life of Daucus carota by inhibiting microbial growth using Phyllanthus niruri extract and zinc oxide nanoparticle during storage at ambient conditions. Suspected pathogenic fungi were isolated from a diseased carrot tuber and was characterized using cultural and morphological characteristics. The in vivo antimicrobial activities of the nanoparticle was tested on the carrot using pin prick method and three pathogenic fungi (Mucor sp., Candida sp. and Aspergillus niger,) were isolated and treated with four concentrations (100%, 75%, 50% and 25%) of 75% Phyllanthus niruri extract/ZnO nanoparticle. Results showed that the treatments promoted disease progress in the carrots compared to the control. This could be attributed to damage caused by the ZnO nanoparticle to the structural and physiological aspects of carrot cells. In conclusion, more detailed research, testing different experimental methods should be done in vivo to prove their synergistic efficacy.