Seed quality has been an important factor in achieving high germination and uniform growth rates in agricultural crops. Meanwhile, pepper plants are moderately sensitive to salt stress at electrical conductivity (EC) in the nutrient solution in the range of 1.2–3.0 dS m−1. We are unaware of any studies regarding the effects of mother plant saline stress on the agronomical quality of pepper seeds. We assessed the effects of three levels of electrical conductivity of the nutrient solution used for mother plant fertigation (2.2, 3.5, and 4.5 dS m−1) on the agronomical quality of pepper seeds (Capsicum annuum L. var. California Wonder). We have analyzed the following seed quality traits: (1) size and weight of seeds and number of seeds per fruit, (2) seed germination and vigor, and (3) chemical composition and histological features of mature seeds. The electrical conductivity treatment of 3.5 dS m−1 caused a statistically significant reduction in the seed size and vigor, as well as partial histological damage to seed endosperm. Moreover, the electrical conductivity treatment of 4.5 dS m−1 caused further reduction in the seed agronomical quality and generalized histological damage to seed endosperm. The electrical conductivity of the nutrient solution used for the fertigation of mother pepper plants should be below 3.5 dS m−1. Future studies should be performed to better gauge the effect of nutrient solutions with electrical conductivity in the range of 2.2–3.5 dS m−1 on the seed quality traits.