This study examined the quality characteristics of 10 different lines of native peppers collected from organic farms in Chungbuk province. The study found a strong correlation between the redness (a*) and ASTA values, which both contribute to the perceived quality of peppers. The highest values were observed in the Iyugsa line. The content of capsaicinoid and beta-carotene also showed a positive correlation, with Chilsungcho having the highest statistically significant value. While the total polyphenol content did not correlate with the other indicators, Chilsungcho again had the highest levels. The Yuwolcho line exhibited the highest ABTS radical scavenging ability, while the Eumseongcho line showed the highest DPPH radical scavenging ability. Taking into account the overall bioactivity quality, Chilsungcho had the highest values in terms of total polyphenol, beta-carotene, capsaicinoid, and redness. It also had the second highest total flavonoid content, ABTS, and DPPH radical scavenging activity, all statistically significant. Therefore, Chilsungcho can be considered an excellent choice when considering physiological activity. Furthermore, this study provides valuable information about the unique characteristics of these 10 native pepper lines, which can assist in selecting the appropriate pepper for food manufacturing and serve as a helpful resource for future research.