The endocrine disruptor bisphenol A (BPA) is one of the most commonly found micropollutants in the environment. However, the biodegradation of BPA under anaerobic (methanogenic) conditions is still an understudied process in wastewater treatment systems. The current study thus addresses the need for a simple and user-friendly analytical method for the rapid and accurate quantification of BPA in complex matrices such as digested and co-digester sludges. We established a microwave-assisted extraction method, followed by derivatization and gas chromatography–mass spectrometry to quantify BPA by comparing it with a deuterated internal standard. The BPA removal capabilities of three digester sludges and three co-digester sludges were examined under mesophilic methanogenic conditions in biogas plants. The endogenous BPA concentration (dry weight) ranged from 1596 to 10,973 µg kg −1 in digested sewage sludges, and from below the limit of quantification to 9069 µg kg −1 in co-digester sludges. When BPA was added to the sludges, the removal capabilities ranged from not significant to 50% after 21 days of incubation. Biogas production was unaffected by the addition of BPA (228 µg kg −1 ) to the aqueous sludge. The study demonstrated that BPA could be removed under anaerobic conditions in accustomed inoculates. The findings have far-reaching implications for understanding BPA persistence and detoxification under anaerobic conditions.