This study provides data on the problem of potential complexation of phenolic compounds synthesized by the plants Solidago canadensis L. and Solidago gigantea Ait. with ammonium forms of nitrogen, partly immobilized in the soil. A comparative analysis of secondary metabolites of the studied plants was performed by HPLC. The leaves of invasively active Solidago canadensis contain nine times more rutin than the plants of Solidago gigantea. Adding to the leaf extracts (v/v1/20) aqueous ammonia solution to pH 8.0 on the chromatograms decreases the intensity or completely causes peaks of flavonoids to disappear; instead, there are peaks of new polar substances (tR 1.5 and 2.0 min). The selective effect of the phenol-ammonium complex on various plant species was revealed. At a concentration of 20 μg/mL, these substances stimulated the formation of lateral roots in soybean seedlings and chrysanthemum cuttings. The suppression of root growth in radish seedlings occurred at a concentration of flavonoids in the extract of 25 μg/mL. In addition, a positive chemotaxis of the Pseudomonas putida (PGPR) was detected in the nitrogen-containing complex based on rutin (5 μg/mL). The identified feature allows PGPR colonization of the root system of Solidago canadensis with corresponding changes in the structure of the microbial community. The ability of the obtained nitrogen-containing polar complexes to regulate the growth processes of plants at extremely low concentration points to promising research in this direction.