Emerging applications of biotechnology may give rise to new uncertainties and uncertain risks. There is a knowledge gap in when an uncertainty should be considered an uncertain risk – we sometimes simply do not know yet. Therefore, regulation concerning biotechnologies should create room to learn what uncertainties entail. However current regulatory structures do not allow for such learning which can hinder innovation. We have organized five stakeholder workshops to shed light on tensions between different stakeholder groups and their different estimates of uncertainties and uncertain risks through a case about the genetic engineering of plants’ rhizosphere. In addition, we have developed a tool for researchers that enables a constructive discussion about emerging risks with a broad range of stakeholders. This tool provides guidelines to identify uncertainties, and develop anticipatory strategies and adaptations in (experimental) research designs to lower or mitigate the earlier identified uncertainties. In addition, this tool helps to identify knowledge gaps for which (additional) risk research should be set up.