A significant part of the innovation activities of firms today is carried out within innovation networks of cooperating enterprises. In such networks, one key challenge is to provide software that enables to systematically share and adaptively integrate knowledge between the partners’ domains of expertise. One potential answer is to apply software applications that allow for end-user or domain expert configuration. We provide preliminary empiric evidence from a field test of an expert-configurable collaborative information system in three innovation networks. In a three-year qualitative study, we have identified challenges to software support originating from knowledge, methodical and relational diversity in the networks. We formulate design challenges and design principles relevant for developing and applying domain expert-configurable software. We provide insights into the significance of related user roles in cooperative innovation projects, and offer the role of ‘facilitators’ as mediating agents in application configuration.