Since 1989 the European Commission’s policy on border regions has slowly shifted focus. Current Interreg policy is increasingly focused upon innovation and cooperation between SMEs. In this paper we question whether this emphasis on firms and innovation neglects the build-up of other kinds of activities and institutions antecedent to effective firm innovation cooperation. We argue that antecedent developments should occur prior to stimulating innovation cooperation between firms, highlighting that building effective environments for regional innovation in cross-border regions encompasses four qualitatively different micro scale phases of development, each requiring qualitatively different policy measures. This four-phase model is applied to a case study of a Dutch-Flemish Interreg programme, using documentary material, a policy-maker survey and a documentary analysis of funded projects to explore incoherences between strategy and reality. We highlight a gap between the strategy’s strong ex ante focus upon innovation, policy-maker perceptions of necessary improvements, and the projects selected for funding.