Introduction Boron is an essential element for higher plants. The symptoms of boron deficiency in plants include cessation of root and leaf growth, necrosis of leaf primordia, necrosis of leaf and stem phloem, bark splitting, or reduced pollen germination. There is a narrow range between boron deficiency and toxicity. Typical boron toxicity symptoms occur in the marginal region of mature leaves, whose portions become chlorotic or necrotic (Ozturk et al., 2010). Pepper (Capsicum annuum L.), as a fresh vegetable, is an excellent commodity containing vitamin C, α-carotene, carbohydrates, flavonoids, and phenols, and it has high antioxidant activity (Russo and Howard, 2002; Serrano et al., 2010; Silva et al., 2013). All the above substances have positive effects on various aspects of human health (Materska and Perucka, 2005). Antioxidants are very important in humans for building cell molecules, since they prevent the oxidizing and harming of cells by reactive oxygen species (Antonius et al., 2014). The antioxidant content is affected by soil management (Antonius, 2014) and the carotenoid concentration of peppers (C. annuum L.) is affected differently in field-grown and greenhouse-grown peppers (Keyhaninejad et al., 2012). Carotenoids serve as antioxidants and participate in the pigment/ protein complex, which harvests light and transfers the energy to chlorophyll (Malkin and Niyogi, 2000), playing a determining role in photosynthesis (Guzman et al., 2010). Many researchers have worked with various aspects of carotenoids in peppers, like carotenoid composition (Collera-Zuniga et al., 2005), carotenoid accumulation in peppers of different colors at ripening (Ha et al., 2007), and carotenoid isomers (Khoo et al., 2011). Flavonoids are ubiquitous in plants with antioxidant activity. The phytochemical changes and antioxidant activity are important dietary attributes in pepper consumption (