The widespread use of hexachlorocyclohexanes (HCH) as pesticides has raised environmental concerns due to their persistence and toxicity. Addressing the pressing need for effective bioremediation strategies, this study explores the effects of α-, β-, δ-, and ε-HCH isomers on the growth, hormonal changes, physiological parameters and bioaccumulation in Alnus glutinosa saplings (1-year-old and 2-year-old) and bacterial communities in polluted soil. A. glutinosa saplings not only withstanded HCH exposure but also enhanced the remediation efficiency by 6.8-24.4%, suggesting an acceleration of pollutant breakdown likely mediated by root exudates positively affecting the soil microbiome. Interestingly, 1-year-old saplings demonstrated greater remediation efficiency post-pruning than unpruned 2-year-old saplings, despite the latter having a larger root biomass. The hormonal analysis indicated that HCH presence led to a reduction in abscisic acid (ABA) and an increase in jasmonic acid (JA), with the magnitude of changes being age-dependent. Salicylic acid (SA) levels increased 1-year-old and decreased in 2-year-old saplings under HCH stress. Moreover, a higher presence of lin-degrading genes in the rhizosphere of treated saplings compared to controls confirmed ongoing biodegradation processes. The outcomes help to better understand the processes involved in degradation of persistent pesticides in soil. The mechanism of in-plant isomerization and the identification of metabolites should be the focus of future research.