Here, we propose organisms from the European Union's (EU) List of Quarantine Pests for regulation as priority pests based on their potential economic, social and environmental impacts in the EU territory. First, a shortlisting methodology was developed to recommend, from the total organisms in the Union Quarantine Pest list, a subset of pests for detailed assessment. Second, expert knowledge was elicited for 46 pests selected by EU risk managers from the shortlisted pests. Third, expert-based estimates of biological parameters were used to inform a multi-criteria analysis. Our methodology combines impacts on economic, social, and environmental domains into a composite indicator, which is used to rank the pests by their expected impacts. The robustness of our recommendation with respect to the uncertainty in biological parameters and the potential diversity of importance given by risk managers to different domains was evaluated. The contributions of the economic, social, and environmental impact-domains to the composite indicator reveal that high potential impact can be driven by diverse profiles. The regulation on priority pests mandates control and monitoring efforts in all EU Member States, which require considerable resources. Our study provides evidence-based decision support to risk managers, to inform decisions on where to allocate the limited resources for plant health surveillance and monitoring. If the list of priority pests is to remain unchanged in size, our results suggest that if based only on impacts, 9 of the 20 currently listed pests should be substituted.