Bell pepper (Capsicum annuum L.); an important spice crop of the region is a rich source of vitamins and antioxidants having many health benefits. Many biotic and abiotic factors contribute towards growth and yield losses of this crop. Arsenic (As) toxicity is a global issue, but it is particularly critical in developing countries. The current study was designed to evaluate the efficacy of selenium (Se) in mitigating the toxic effects of As in two varieties (HSP-181 A and PS09979325) of Capsicum annuum L. Different concentrations of As (0, 50, and 100 µM) and Se (0, 5, and 10 µM) were tested using 14 days old seedlings of C. annuum L. The As stress caused a significant (P ≤ 0.001) reduction in growth, uptake of nutrients, and eco-physiological attributes in both varieties however, the response was specific. While the overproduction of osmo-protectants and antioxidants intensified the symptoms of oxidative stress. The maximum reduction in shoot length (45%), fresh weight (29%), and dry weight (36%) was observed in under 100 µM As stress. The organic acids exudation from the roots of both cultivars were significantly increased with the increase in As toxicity. The Se treatment significantly (p ≤ 0.001) improved growth, nutrient uptake, gas exchange attributes, antioxidant production, while decreased oxidative stress indicators, and As uptake in the roots and shoots of all the subjects under investigation. It is concluded from the results of this study that Se application increased photosynthetic efficiency and antioxidant activity while decreasing As levels, organic acid exudation, and oxidative stress indicators in plants. Overall, the var. PS09979325 performed better and may be a good candidate for future pepper breeding program.