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Abstract Purpose Biofilm-active antibiotics are suggested to improve the outcome of implant-associated infections; however, their role in infections after spinal instrumentation is unclear. Therefore, we evaluated the outcome of patients with spinal implant-associated infections treated with and without biofilm-active antibiotics. Methods The probability of infection-free survival was estimated for treatment of spinal implant-associated infections with and without biofilm-active antibiotics using the Kaplan–Meier method; Cox proportional-hazards regression model was used to identify factors associated with treatment failure. Results Among 93 included patients, early-onset infection was diagnosed in 61 (66%) and late-onset in 32 infections (34%). Thirty patients (32%) were treated with biofilm-active antibiotic therapy and 63 (68%) without it. The infection-free survival after a median follow-up of 53.7 months (range, 8 days-9.4 years) was 67% (95% confidence interval [CI], 55–82%) after 1 year and 58% (95% CI 43–71%) after 2 years. The infection-free survival after 1 and 2 years was 94% (95% CI 85–99%) and 84% (95% CI 71–93%) for patients treated with biofilm-active antibiotics, respectively, and 57% (95% CI 39–80%) and 49% (95% CI 28–61%) for those treated without biofilm-active antibiotics, respectively (p = 0.009). Treatment with biofilm-active antibiotics (hazard ratio [HR], 0.23, 95% CI 0.07–0.77), infection with Staphylococcus auras (HR, 2.19, 95% CI 1.04–4.62) and polymicrobial infection (HR, 2.44, 95% CI 1.09–6.04) were significantly associated with treatment outcome. Severe pain was observed more often in patients without biofilm-active antibiotic therapy (49% vs. 18%, p  = 0.027). Conclusion Treatment with biofilm-active antibiotics was associated with better treatment outcome and less postoperative pain intensity.