Abstract Adaptability is vital in today’s rapidly changing business environment, especially within IT. Agile methodologies have emerged to meet this demand and have thereby gained widespread adoption. While successful in smaller, co-located teams and low-criticality projects, applying agile methods in broader contexts poses challenges. Nevertheless, many organizations have started implementing agile methodologies in various areas, including large-scale Enterprise Resource Planning (ERP) projects. In contrast to traditional development, ERP projects involve deploying extensive integrated systems, are substantial in scale, and entail high risks and costs. Accurate predictions, like effort estimations, are crucial to meet customer satisfaction and deliver within plan and budget. However, estimating effort in an agile environment poses its own set of challenges. For instance, coordination efforts and dependencies among teams must be considered. While effort estimation is well-explored in classical software development and small-scale agile contexts, limited research exists in large-scale agile settings, particularly in projects rolling out and customizing standard ERP solutions. To address this gap, we conducted a case study on effort estimation in a large agile ERP transformation program, describing the estimation process, highlighting challenges, and proposing and evaluating mitigations.