Objective: To evaluate the effect of pruning on the agronomic variables and fruit quality of habanero peppers (Capsicum chinense Jacq.). Methodology: Habanero peppers were pruned with two intensities, two shoots and three shoots. The control plants were not pruned. The experiment had a randomized block design with four replications. The experimental plots consisted of 50 plants established in rows at a distance of 1.2 m and 0.3 m among plants within a row. The evaluated variables were fruit yield, number of fruits per plant, fruit weight, fruit length and fruit diameter. Data were obtained from 10 harvests. For the analysis, the fruit quality, ash content, moisture, protein and crude fiber were determined. Results: Plants with two and three shoots produced fruits of 4 and 3.99 cm in length. Plants with two and three shoots produced 42 and 48% first quality fruits, whereas control plants produced only 10% first quality fruits. The highest protein content in fruits at physiological ripeness (14%) and commercial maturity (12%) was observed in plants pruned to two shoots. Implications: These results show the importance of crop management on the fruit quality of habanero peppers. Further studies are needed to have more information on the effects of crop management on the nutritional content of fruits. Conclusion: The pruning of habanero pepper plants significantly influenced the fruit size, crude fiber and protein content in their fruits.