Collaborative R&D projects are often associated with high degrees of complexity and uncertainty and consequently they are difficult to manage. The purpose of this article is to identify and analyse which motives collaborating companies have when engaging in inter-organizational R&D projects, and how these motives subsequently affect the selection of control mechanisms. Empirically, the paper draws on two case studies of joint R&D projects in the process industry. Findings indicate that companies have two main motives to engage in joint R&D projects. If the primary motive was financial, e.g. to reduce costs, formal control mechanisms such as contractual obligations and formal planning were preferred before informal ones. If, on the other hand, relational motives such as building long-term relations were the primary aim, a different logic applied. Under such conditions, informal control mechanisms tended to be used (e.g. trust and joint decision-making). The paper adds to the growing body of literature on collaborative R&D projects and gives management advice on how to manage joint R&D projects.