Selenium (Se) and zinc (Zn) are essential antioxidant enzyme cofactors. Foliar Se/Zn application is a highly effective method of plant biofortification. However, little is known on the effect of such applications on the accumulation of phytochemicals with pro- or antioxidant related activity in pea (Pisum sativum L.). A two-year pot-experiment was conducted to examine the response of pea varieties (Ambassador, Premium) to foliar-applied sodium selenate (0/50/100g Se/ha) and zinc oxide (0/375/750g Zn/ha) at the flowering stage. Concentrations of Se and Zn, total phenolic content (TPC), total flavonoid content (TFC) and total antioxidant activity (ABTS, FRAP) of seeds were determined. Selenium treatments improved seed Se accumulation in both varieties dose-dependently (p < 0.001). Premium variety accumulated greater amounts of Se in seeds than Ambassador variety. Highest Se accumulation was found in seeds of Premium treated with 100 g Se/ha (7.84 mg/kg DW) vs. the control (0.16 mg/kg DW). Contrarily, seed Zn accumulation was not significantly affected by foliar-applied zinc oxide. Selenium and zinc treatments positively influenced TPC (p < 0.001) and in part ABTS (p = 0.004) and FRAP (p = 0.006) of Ambassador. The highest TPC was found in Ambassador treated with 100 g Se/ha and 750 g Zn/ha (2926 and 3221 mg/100 g DW, respectively) vs. the control (1737 mg/100 g DW). Selenium at 50 g/ha increased TFC vs. the control (261 vs. 151 mg/100 g DW) in Premium (2014 growing season, p = 0.023). Overall, the most pronounced effects that were found for both Se and Zn were improved total phenolic contents. The results are important for producing pea/pea products rich in health-beneficial bioactive plant compounds.