Accurately estimating Origin–Destination matrices is a pressing challenge in transportation management and urban planning. However, traditional methods like travel surveys have limitations in availability and comprehensiveness, which have been further exacerbated by the recent changes in mobility patterns induced by the COVID-19 pandemic. To address this issue, we focused on the Trenord railway network in Lombardy, Italy, and developed an innovative pipeline to integrate ticket and subscription sales and Automated Passenger Counting data using the Iterative Proportional Fitting algorithm. By effectively navigating the complexities of diverse and incomplete data sources, our approach showcases adaptability across various transportation contexts. Our research offers a valuable tool for operators, policymakers, and researchers, bridging the gap between data availability and the need for precise OD matrices. Additionally, we emphasise the potential of dynamic OD matrices and showcase methods for detecting anomalies in mobility trends, interpreting them in the context of events from the last months of 2022.