This study examines structural incongruences between organizational and product domains and their implications for coordination effectiveness in large-scale software development. We use the ongoing shift from on-premise to cloud-based software solutions to examine longitudinal effects of structural incongruences, i.e. the mismatch between organizational structures, including knowledge and task dependencies, and product structures, including technical dependencies, and how they resolve. We integrate extant literature in this field with literature on multiteam systems (MTS) and team composition to guide our longitudinal case study of one particular MTS within a large software organization. First insights from an initial case study of three development teams of different MTSs show how high level structural incongruences emerge on a team-level, providing a foundation for our subsequent study. By exploring the effects of structural incongruences over time, we expect to contribute to existing literature on organizational and product structure alignment as well as on MTS coordination effectiveness research.