In today's business environment, value creation is a collaborative effort in which companies depend on a number of external stakeholders. This implies a shift towards inter-organizational relationships and dependencies between companies. In this shift, companies seek strategies for how to effectively coordinate standardization efforts, share maintenance costs, and engage in open innovation initiatives, while at the same time increase control and accelerate development of differentiating functionality. On the basis of a multi-case study in six B2B software development companies, this paper explores the challenges involved in managing different ecosystem types. Based on the 'Three Layer Product Model' [1], we distinguish between innovation ecosystems, differentiating ecosystems and commoditizing ecosystems. We outline the challenges the companies experience in managing these, and we develop a model in which we identify the drivers, the purpose, the stakeholders and the characteristics of each ecosystem type.