In the plant body, phenolic compounds nonspecifically affect the processes of morphogenesis and perform a wide range of regulatory and protective functions. Of particular interest are the processes involved in the complexation of flavonoids as a result of their interaction with ammonium forms of nitrogen. Polar compounds, which are formed in tissues as a result of chemical transformation, are quite mobile in soil solutions and show high biological activity. The properties of phenol-ammonium complexes are of considerable interest in terms of morphogenesis, physiology of stability, as well as in the system of interaction of plants with soil microorganisms. Studies of the effect of phenol-ammonium complex were performed on seeds and seedlings of Scots pine. Quantitative indicators of germination energy and germination were determined by seed germination. Biochemical profiling of seedling tissue extracts was performed by high-performance thin layer chromatography. It has been experimentally confirmed that rutin (quercetin-3-O-rutinoside) after interaction with 10% aqueous ammonia solution forms a complex of substances, among which the chromatography revealed polar products that potentially affect the regulation of growth. At a total concentration of 15 mg/l, these substances significantly increased germination energy and seed germination. In pine seedlings, they stimulated the growth of roots and shoots. The effect of the complex of organic compounds on seedlings depended on the concentration, duration of seed treatment and had a prolonged effect. The obtained phenol-ammonium complex at a concentration of 10-15 mg/l contributed to an increase in the amount of chlorophylls, carotenoids in the tissues of seedlings, and at 20-40 mg/l increased the content of phenolic synthesis products.