Collaboration between regional stakeholders is increasingly emphasized in innovation policy as a way to activate the inherent agency in a regional innovation system. Partnerships of diverse stakeholders have been identified as critical, being able to envisage and implement future pathways that in turn bring change to a region. Thus, the knowledge of various stakeholders is supposed to be combined in novel ways in order to define regional assets and possible future pathways. Nevertheless, it has been recognized that these agency activation approaches often fail to realize these long-term visions initially agreed by partners. We here draw on Sotarauta’s notion of policy ‘black holes’, where regional partners repeat past superficial successes rather than driving in to systemic change. We seek to understand the conditions under which regional stakeholders can build realistic and adaptable strategies that shift regional development trajectories. We explore this via a qualitative approach comparing entrepreneurial discovery processes in three peripheral regions, namely Twente (Netherlands), Aveiro (Portugal) and Lincolnshire (UK). We reflect on the potential value of more effectual (opportunistic/ flexible) approaches to entrepreneurial discovery. We argue that black hole problems may arise from the way agency activation strategies conceptualize long-term strategy development, if partners’ mind-sets are too causal and lacking flexibility to continually reorient strategies during implementation better towards these collective visions.