The widely used antibiotic oxytetracycline (OTC) is found in various natural and engineered water environments, where it can potentially disrupt important ecosystem functions such as nitrification. This work proposed the use of alkaline-pretreated biochar (BC) with a nitrifying microbiome to mitigate OTC disturbance and enhance the removal and detoxification of both OTC and its by-products (BPs). The OTC adsorption capacity of BC was preoptimized using a 1 M NaOH solution. While exposure to OTC led to the replacement of the dominant sub-species populations within Nitrosomonas, the addition of BC preserved the original diversity and structure of the nitrifying microbiome. The evaluation of long-term reactor operation and batch tests using advanced analytical methods revealed that the addition of BC significantly increased the removal of OTC with a novel biotransformation pathway. Structure-based toxicity modeling and antimicrobial susceptibility experiments were performed to assess the toxicity of OTC, its BPs, and bulk effluent containing both OTC and its known/unknown BPs. Three OTC BPs were found to have 6-90 times higher toxicity than OTC itself. In comparison to the microbiome alone, the addition of BC had the potential to enhance the detoxification of both OTC and its BPs. Collectively, the results of the present study indicate that the addition of BC to nitrifying systems may be a promising retrofitting option that proactively maintains the biological function and stability of the system in the presence of toxic waste streams via the synergistic control of both the original contaminants and their BPs in conjunction with nitrifying microbiomes.