Drug-induced liver injury (DILI) is a major concern associated with the use of avacopan, a new therapeutic agent for antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Here, we report a rare instance of liver biopsy performed for persistent liver injury following discontinuation of avacopan in an elderly woman with microscopic polyangiitis (MPA). The patient developed cholestatic liver injury after 2 months of avacopan therapy, which led to drug cessation. Despite the discontinuation of avacopan followed by supportive care, the liver enzyme levels remained elevated, necessitating liver biopsy. Histological examination revealed residual inflammation and focal necrosis around the portal vein, indicating ongoing liver injury despite avacopan withdrawal. This case report highlights the hepatotoxic potential of avacopan, the importance of vigilant liver function monitoring, and the value of liver biopsy in the chronic phase of avacopan-induced liver injury. Further research is required to elucidate avacopan hepatotoxicity mechanisms and identify potential risk factors for DILI in patients with AAV.