Due to widespread selenium deficiency in food the aim of this study was to evaluate the effectiveness of a new Se(II)-containing organic chemical compound 2-iminoselenazolidin-4-ones (ISeA) in the form of a nanoscale associate (1–5 nm) solution for Swiss chard and komatsuna plants biofortification. Application of the chosen substance as a foliar treatment (2 mg·L−1) and as an additive to a hydroponic nutrient solution (10 mg·L−1) was performed. Both cultures had a high level of Se absorption, distribution and accumulation in leaves two or more times greater than in petioles. Se content in chard petioles (15 mg·L−1) when applying ISeA as a component of the nutrient solution exceeded the accumulation of Se during foliar treatment (9.6 mg·L−1) and the same trend in the komatsuna leaves was observed. When applying ISeA to the nutrient solution, an increase in komatsuna and chard biomass was seen at 36 and 68% and for leaf treatment by 21 and 45%, respectively. For komatsuna and chard an increase in the ratio of dry to fresh weight was also observed to be 27 and 26%, and for foliar treatment—0 and 16%, respectively. Treatments led to increase in chard plants height (7–17%), enlargement of leaves (19–42%), a rise in photosynthetic pigments (20–60%) and anthocyanin (2.9 and 2.2 times) concentration, and for komatsuna—the multiplication of leaves number (28%) and their surface area (27–29%) as well as a rise in the concentration of anthocyanin (1.0 and 1.6 times) with foliar treatment and nutrient solution enrichment.