Abstract Rapid urbanization is placing increased pressure on natural, restored and designed ecosystems to provide services to growing human populations. The establishment and spread of invasive alien species within and around urban areas threaten biodiversity and ecosystem functioning, and the services they provide. Consequently, there is a need to protect and manage areas where invasions will have the greatest socio‐ecological impact. Limited resources call for the strategic prioritization of these areas, yet there are few widely adopted, standardized approaches for prioritizing sites vulnerable to species invasions in urban areas. We applied multi‐criteria decision analyses in a geographic information system to develop a strategic, spatial prioritization approach for identifying those sites most sensitive to terrestrial alien plant invasions. To test this approach, we use the Toronto region as a case study, the most populous metropolitan area in Canada and one of the fastest growing urban centres in North America. Through consultation with local conservation authorities, we developed an objective, hierarchical set of 19 criteria grouped into two categories: biodiversity and ecosystem functioning, and ecosystem services. Spatial data layers were assigned to each criterion and used to map areas most important for biodiversity and ecosystem functioning and providing ecosystem services. We overlayed these priority areas with distribution data of Vincetoxicum rossicum, one of the Toronto region's most widespread and damaging invasive alien plant species (IAPs) to determine the potential threat species’ invasions pose to these important areas. High‐priority sites identified by our prioritization model include areas of significant biodiversity conservation value such as intact forests, meadows and wetlands which are crucial for providing regulating and supporting services. Our IAPs distribution map showed that these high‐priority sites are heavily invaded (92.9% of the area occupied by V. rossicum comprises medium‐high‐priority sites) and should be prioritized for management to ensure biodiversity and ecosystem functioning and the provision of ecosystem services are maximized. The approach applied in this study can be useful for conservation practitioners in guiding the selection of high‐priority, socio‐ecologically significant sites for management action in urban landscapes across different geographic regions and spatial scales.