This article presents the results of a study on the impact of long-term cultivation of energy crops (Silphium perfoliatum L., Sida hermaphrodita (L.) Rusby, Miscanthus × giganteus) on the microbiota of grey forest soils in the Western region of Ukraine. The relevance of investigating changes in microbial communities is substantiated by the growing implementation of energy crops as alternative sources of bioenergy and as tools for the ecological stabilization of agro-landscapes. The analysis included the abundance of major physiological groups of microorganisms: ammonifiers, amylolytics, oligonitrotrophs, oligotrophs, pedotrophs, humate-transforming, and cellulolytic organisms. It was established that after more than twenty years of energy crop cultivation, the abundance of most microbial groups increased by 1.3-2.5 times compared to soils under traditional crop rotation. The most pronounced positive effect was observed under Sida hermaphrodita, which contributed to the highest increase in soil biogenicity. At the same time, soils under Miscanthus × giganteus and Silphium perfoliatum showed moderate enrichment of microbial complexes along with a reduction in the activity of cellulolytic organisms. The study concludes that long-term cultivation of energy crops does not lead to degradation of the microbiological condition of grey forest soils but rather enhances their biogenic activity and can be considered a promising strategy for the environmentally sound use of marginal lands.