Anaerobic digestion plays a crucial role in the transition toward a circular economy. Incorporating system supervision through mathematical modelling can enhance control and resilience. This study aims to assess the impact of scheduled digester maintenance on the effectiveness of modelling as a tool for monitoring and control. Data from a pilot-scale plug-flow digester were analyzed using an adapted ADM1 model. The maintenance involved halting the digester and removing sedimented solids. Model calibration indicated solid retention in the first two zones of the reactor, while the hydrolysis coefficient and biogas potential remained at 0.122 d−1 and 100.4 mL CH4/gVS, respectively. The average biogas production decreased from 156 to 109 mL/gVS pre- and post-maintenance. Simulations showed a decline in the model’s predictive accuracy after maintenance. To improve model fit, the initial conditions, solids retention, and kinetic parameters were adjusted. Optimal performance was achieved with khyd at 0.045 d−1 and B0 at 52.28 mL gVS−1, revealing an issue with the digester’s heating system. In conclusion, maintenance can significantly alter digester conditions, requiring model recalibration to maintain its effectiveness as a digital copilot for process supervision.