This paper has investigated the practice of E-Commerce portal named Metrotarkari for marketing vegetables and fruit items in Kathmandu valley. A case study approach underpinned the study so as to identify current issues and practice of E-Commerce portal for vegetable and fruit items thereby adopt appropriate strategies for its sustainability in this sector. The study used explanatory form of analysis on the issues of business model, payment system, distribution system, overall challenges and marketing strategies based on the face to face interview with chief operating officer of Metrotarkari. The result shows that their B2B feature is serving more customers than B2C feature does in daily basis. The cash on delivery has been the preferable option of payment system although they have facility of Paypal, E-Sewa and Sctmoco. The main reason behind the problem in maintaining and delivering quality items is the lack of their own inventory and their dependency on others vendors. Establishing their own cold store or inventory and appending the C2C feature in their existing portal are major suggestions made to provide benefit to farmers and customers thereby sustain in this sector.