An experiment was conducted in a poly-house along with an open field at Instructional Farm, College of Agriculture, Vellayani, Thiruvananthapuram, Kerala, during March 2013 to September 2013 to study the performance of chilli (Capsicum annuum L.) varieties viz. Vellayani Athulya, Jwalamukhi and Anugraha and the effect of fertigation on productivity of chilli under protected cultivation. The plants grown under poly-house and the plants grown with fertigation recorded maximum shelf-life, ascorbic acid content and capsaicin content. Maximum shelf-life and ascorbic acid content were recorded by plants grown under poly-house with fertigation. Among varieties, Vellayani Athulya showed maximum shelf-life and ascorbic acid content. Vellayani Athulya under poly-house recorded maximum shelf-life and ascorbic acid content of fruit. Vellayani Athulya grown with fertigation also recorded maximum ascorbic acid content. The maximum shelf-life and maximum ascorbic acid content were recorded by Vellayani Athulya grown under poly-house with fertigation while, maximum capsaicin content was recorded by Jwalamukhi grown under poly-house with fertigation.