To investigate the recovery mechanisms of anaerobic ammonium oxidation (anammox) systems under long-term yttrium (Y) stress, we established two recovery strategies: natural recovery (R1) and biochar-mediated recovery (R2). Compared with natural recovery, biochar addition significantly enhanced total nitrogen removal and anammox activity by 20.85% and 55.72 mg N/(gVSS·d), respectively. Extracellular polymeric substances in the sludge increased by 115.72 mg/g VSS, with polysaccharides contributing an additional 80.13 mg/g VSS, serving as a biological barrier against Y-induced stress. Zeta potential decreased by 2.5 mV, promoting sludge aggregation. Microbial community analysis revealed that biochar selectively enriched anammox bacteria (Candidatus_Brocadia) and symbiotic genera (Exiguobacterium and Norank_f_Aggregatilineaceae), whose relative abundances increased by 13.82%, 19.55%, and 4.17%, respectively, establishing a stable ”core–defense–structure” consortium that enhanced system resilience under Y stress. Functional gene analysis indicated that biochar alleviated Y-induced electron flux limitations by upregulating genes involved in quinone pool synthesis (ubiE), complex III function (petB/C), and cytochrome c-associated pathways (ccoP, cycB). Differential protein and metabolite enrichment analyses further demonstrated that biochar promoted ribosomal protein translation, enhanced quorum sensing, enriched ABC transporters, increased antioxidant metabolites (3',4'-Dimethoxy-2'-Hydroxychalcone and Dihydrolipoate), and reduced intracellular toxin accumulation (Neosaxitoxin). These synergistic effects repaired damaged anammox cell structures, mitigated intracellular oxidative stress, improved substrate utilization and Y efflux, and redirected more energy toward anammox metabolism, thereby restoring bacterial functional performance. This study provides a theoretical and technical foundation for sustainable, low-carbon treatment of yttrium-laden wastewater in southern Jiangxi.