This paper describes a generic design pattern to introduce organizational mechanisms into multi-level agent-based simulation architectures, to help the modelling of highly structured complex systems. This pattern makes it possible to specify how to couple any three levels of agents in a multi-level simulation architecture, through their relationships to environments, taking into account organizational constraints. As a proof of concept, we applied this pattern to the fine-grained modelling of batch management in pig farms, and illustrate how the pattern can be instantiated and composed at several agent levels to accurately handle a complex organization in time and space. We thus demonstrate the benefits of combining organizational concepts and multi-level patterns to represent and simulate complex dynamic systems.