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Peppers are a rich source of diverse bioactive compounds with potential health-promoting properties. The levels of bioactive compounds and antioxidant activity can be affected by analytical methods, pre-harvest factors, and the quality of peppers. In order to understand the nutrient composition and antioxidant activity in peppers, determination of factors influencing the contents of bioactive compounds is important. The overall objectives were to determine the efficient conditions of sample preparation and the impact of pre-harvest factors affecting bioactive compounds and antioxidant activity. Optimal extraction procedures were developed, and HPLC methods were validated for bioactive compounds in peppers. The highest flavonoids were extracted in ethanol, while myricetin was extracted using N-N-dimethylformamide. Optimized conditions for flavonoids were obtained during 3 h of extraction time and hydrolysis in M HCl for 60 min at 95 degrees C. Capsaicinoids and ascorbic acid were simultaneously separated and extracted using a solvent mixture consisting of 3% metaphosphoric acid: ethanol (2:8) after 30 min of sonication. To determine the relationship between bioactive compounds and antioxidant activities in pepper extracts from different solvent properties, bioactive compounds were analyzed, and the antioxidant activities were assayed by 2,2,-Diphenyl-1-picryl hydrazyl (DPPH), reducing power, and degradation of deoxyribose. Hexane extracts had the highest levels of capsaicinoids and carotenoids, while methanol extracts had the highest levels of flavonoids. Strong DPPH scavenging activity and reducing power were found in lipophilic extracts, while hydrophilic extracts were appropriate for inhibition of deoxyribose degradation. Variation in content of ascorbic acid, capsaicinoids, and flavonoids was evaluated at immature and mature stages of pepper cultivars in different locations over two years. Mature peppers contained the highest levels of capsaicinoids and ascorbic acid. Flavonoids were variable at different maturity stages. Interactions between pre-harvest factors and bioactive compounds were highly significant. This study demonstrated the efficient sample preparation methods and simultaneous separation of bioactive compounds, which reduces analysis time and leads to reduced cost. The antioxidant properties were strongly associated with the concentration of bioactive compounds based on selective pepper extracts. The pepper quality can be improved by using appropriate pre-harvest conditions that increase the levels of bioactive compounds in peppers.