The influence of low-intensity electromagnetic radiation (EMR) on the content of phenolic compounds (PC) in plants on different stages of ontogeny is discussed. A medicinal plant (Calendula officinalis L.) and agricultural crop Fagopyrum sagittatum G., diploid varieties and tetraploid varieties were chosen as objects of study. Microwave EMR in two frequency bands, 53.57-78.33 GHz (wide range mode) and 64.00-66.00 GHz (narrow range mode), has been selected to learn the physical effects on seeds, with a treatment exposure time of 20, 12, or 8 min. The experiments were conducted under laboratory and field conditions. Treated and control seeds were germinated by 100 pcs in a growth chamber on moistened filter paper at 22–24˚C in the dark and placed on the daylight from the third day. The level of PC in the seedlings was measured with the Folin-Ciocalteu reagent. It was found that in the EMR pretreated C. officinalis seedlings the level of PC is maximal on 14th day of germination. The wide mode treatment for 12 min results in a two-fold increase in the level of PC in juvenile shoots with respect to control. Different constitutional levels of phenolic compounds in the leaves of diploid and tetraploid varieties of F. sagittatum in the most critical phases of ontogeny were found. It is recommended to use EMR with a 12 min exposure time for C. officinalis. The narrow frequency mode with an exposure time of 20 min is preferable to use for most varieties of F. sagittatum.