The aim of this work was to investigate the changes of the content of polyphenols in fruits of Capsicum chinense Jacq. at different harvest times and their correlation with the antioxidant activity. Habanero pepper plants grown in black soil (Mayan name: Box lu’um) and harvested at 160, 209, 223, 237 and 252 post-transplant days (PTD) were analyzed. The results indicated that subsequent harvesting cycles decreased the content of total polyphenols, catechin, chlorogenic acid and ellagic acid, while the content of gallic and protocatechuic acid increased. The antioxidant activity determined by DPPH (2,2-Diphenyl-1-picrylhydrazyl) radical scavenging and ABTS (2,2′-azino-di-3-ethylbenzthiazoline sulfonic acid) assay decreased through the harvest days. Linear correlation analysis between total polyphenol content and antioxidant activity in peppers resulted in a correlation of r2DPPH = 0.8999 and r2ABTS = 0.8922. Additionally, a good correlation of the antioxidant activity was found with catechin (r2DPPH = 0.8661 and r2ABTS = 0.8989), chlorogenic acid (r2DPPH = 0.8794 and r2ABTS = 0.8934) and ellagic acid (r2DPPH = 0.8979 and r2ABTS = 0.9474), indicating that these polyphenols highly contributed to the antioxidant activity in Habanero peppers. This work contributes to understanding the changes that take place during the development of Capsicum chinense, indicating that fruit harvested at earlier PTD showed the highest concentrations of total polyphenols and antioxidant activity, obtaining the best results at 160 PTD.