A pot experiment was conducted during 2013-14 at Chaudhary Charan Singh, Haryana Agricultural University, Hisar  to evaluate  the effect of non-conventional chemical viz., salicylic acid, zinc sulphate, magnesium sulphate, indole acetic acid, indole butyric acid and fungicide viz., carbendazim, on total phenol, flavonol, tannin and electrolyte leakage of red fruits of chilli varieties (susceptible- Pusa Jwala and resistant- Sadabahar) against Colletotrichum capsici the causal agent of fruit rot in chilli. The phenol content was increased significantly in both the varieties (resistant and susceptible) when sprayed with salicylic acid followed by pathogen as compared to other non-conventional chemicals at 24 and 48 hours intervals. The increase in total phenol was more pronounced in resistant variety (7.84 mg/g fresh weight) after 48 hours, when sprayed with salicylic acid at 5mM concentration. Flavonol content was higher in uninoculated red fruits of susceptible variety (1.50 mg/g fresh weight) as compared to resistant (1.37 mg/g fresh weight). Tannin content was higher in resistant (3.71 mg/g fresh weight) as well as susceptible (3.09 mg/g fresh weight) varieties after inoculation than uninoculated varieties (1.38 and 1.02 mg/g fresh weight, respectively) at 5mM concentration. The activity of electrolytes was more pronounced in resistant variety as compared to susceptible variety when sprayed with non-conventional and fungicide in all the concentration. Electrolytes leakage was more when sprayed with fungicide as compared with salicylic acid 5mM concentration after 48 hours of pathogen inoculation.