Electroporation significantly impacted plant growth and the content of flavonoids, especially baicalein and wogonin, depending on the treatment parameters. Concentrations of aglycones were increased in at least half of the treatment conditions. The greatest amounts (a 2.5-fold increase compared to controls) were recorded after applying an electrical field characterized by the following parameters: E = 3 kV/cm, t = 100 μs, and N = 10. In conclusion, electrostimulation is an innovative and efficient way to increase plant growth and yield in an aeroponic system, as well as modulate the profile and content of bioactive flavones in the roots. However, the fine-tuning of these parameters, such as the electrical field strength (E), length (t), and number (N) of impulses delivered, is of great importance. It was also shown that cultivation of the experimental plants in aeroponics had a positive impact on their survival and development while being a sustainable and efficient horticultural practice.