Malnutrition, heart, respiratory and pulmonary diseases are becoming most critical in Mid Himalaya. Vegetables rich in micronutrients, antioxidants and bioactive compounds can help to solve the issue. Sweet pepper is one of the best choices but as it is a warm and humid loving crop and bioactive compounds are highly varied with attitude and temperature condition, the study was conducted to identify promising antioxidant rich sweet pepper lines adapted to hill condition. Thirty eight advanced breeding lines (ABLs) of sweet pepper were evaluated for variations in total polyphenol, total carotenoids, ascorbic acid and antioxidant activity in mid Himalayan region. Antioxidant activity was measured using two in vitro assays viz. 2, 2-diphenyl-1-icrylhydrazyl (DPPH) 2, 2′-Azino-bis(3-Ethylbenzothiazoline-6-Sulfonic Acid) (ABTS). Additionally colour parameter capsanthin, pungency compound capsaicin and fruit firmness were evaluated. Among ABLs, significant differences (p ≤ 0.05) were obtained with respect to antioxidant composition and antioxidant activity. Ascorbic acid and total phenol varied from 39.42–85.12 mg/100 g and 13.01–71.24 mg GAE/100g fresh weight (fw) respectively, while ABTS % Inhibition and DPPH % Inhibition varies from 10.95–80.05 and 11.19–49.18 respectively. Chemometric tools like principal component analysis (PCA) and agglomerative hierarchical clustering (AHC) were applied to understand possible classification sweet pepper ABLs based on bioactive antioxidant compounds, antioxidant potentiality and fruit firmness. PCA revealed that the first two components represented 67.78% of the total variability in the total variation. AHC classified cultivars into four main groups on the basis of the measured parameters. Results suggested that VLCP-16-1, VLSM-3 and Mukteshwar for Vitamin C; VLCP-16-57, VLCP-16-54, Mukteshwar and VLCP-16-52 for polyphenols, VLCP-16-54, VLCP-16-57, VLCP-2016-52 and showed highest antioxidant activity. The result will help in advance breeding of sweet pepper for development of nutritionally rich varieties.