The AGMEMOD Partnership seeks to capture the inherent heterogeneity of the agricultural systems existing by combining individual country models of 27 EU Member States and several accession countries into one single model while still maintaining analytical consistency. Although this approach facilitates the comparison of the impact of a policy across different Member States, it generates challenges in practical implementation, ranging from high communication and administration requirements to aggregation and consistency issues. This contribution provides insights into the different challenges posed to the scientists and discusses the key issues for maintenance and further development of such a complex system. Specific attention is paid to technical devices and tools as well as to the design of institutional settings for avoiding inconsistencies.