Post-harvest spoilage of Amla fruits is one of the major problems which reduces the economic quality of the fruits. The goal of the present study was to identify the post-harvest fungal pathogens associated with Amla fruits based on morphological and molecular characteristics, growth characteristics of the fungi, and their eco-friendly control measures. The fungi were identified as Penicillium rolfsii Thom., Penicillium herquei Bainier & Sartory, Aspergillus aculeatus Iizuka, Aspergillus terreus Thom., and Mucor sp. Frasen. Penicillium rolfsii and Aspergillus aculeatus were preferred to grow on Richard Agar medium; Penicillium herquei grew the maximum on Potato Sucrose Agar medium; Aspergillus terreus was found to grow irrespective of culture media and Mucor sp. grew on all the tested media except Richard Agar medium. The optimum temperatures were recorded at 25 to 35℃ for all of the fungi except Mucor sp., which preferred to grow at 15℃. Aspergillus aculeatus was able to grow on a broad range of pH (5 to 9); Penicillium rolfsii, Penicillium herquei, and Aspergillus terreus were grown better at neutral to slightly alkaline pH, while Mucor sp. on slightly acidic conditions. Aqueous crude extracts of garlic and black cumin were found to show inhibitory activity against all the fungi. Food preservative sodium benzoate was found to be the most efficient against fungal pathogens. Based on our findings, it is suggested that garlic extract and sodium benzoate could be used to manage the fungal growth associated with post-harvest Amla fruit diseases.