Phthalic acid esters (PAEs), as persistent organic pollutants, alter soil microbial communities, with long-term implications for ecosystem function. This study examined microbial responses to PAEs contamination and the role of biochar (BC) amendment in promoting microbial resilience and succession. PAEs' exposure led to modest reductions in dominant bacterial phyla (Firmicutes, Proteobacteria, Actinobacteriota) and increased pollutant-degrading groups such as Bdellovibrionota, Cyanobacteria, and Nitrospirota. Key nutrient-cycling phyla (Acidobacteriota, Chloroflexi) declined, indicating disruption of carbon and nitrogen turnover. Short-term BC application promoted plant growth-promoting and decomposer taxa (e.g., Alicyclobacillaceae, Oxalobacteraceae), suppressed opportunistic pathogens, and partially restored microbial functionality through direct (sorption, habitat) and indirect (pH, enzyme activity) mechanisms. Fungal communities showed higher sensitivity to both PAEs and BC. While BC reduced overall fungal diversity, it increased stress-tolerant taxa such as Gibellulopsis piscis and Solicoccozyma. Long-term BC amendment, especially post-cultivation, triggered microbial succession favoring K-strategists, particularly Actinobacteria, due to their ability to degrade biochar-derived aromatic compounds and thrive in alkaline, carbon-rich soils. Though bacterial diversity recovered partially after lettuce cultivation, some beneficial genera (e.g., Massilia, Sphingomonas) declined, and unclassified taxa expanded significantly, reflecting lasting ecological shifts. Strong β-diversity changes suggested a transition toward a more specialized and resilient microbial community. Overall, biochar demonstrates strong potential as a long-term soil amendment in PAEs-contaminated environments by enhancing detoxification and supporting microbial recovery. However, the observed trade-offs in diversity and community composition highlight the need for careful, long-term monitoring to ensure sustainable bioremediation outcomes.