Non-indigenous species have been widely recognized as major drivers of biodiversity loss. However, management in marine ecosystems entails particular challenges of detection and control, with an approach which requires stakeholders from the government, academia and the public. To generate a first approach to what should be the national Chilean agenda for non-indigenous species (NIS) management, a workshop was convened at the Universidad Católica del Norte in Coquimbo on the past, present and future of marine bioinvasions in Chile. The workshop, with more than 60 participants, including academics and public services, gathered information from the published literature on the state of the art of marine bioinvasions in Chile and proposed a work agenda for the coming years. The results highlight that the design and implementation of more focused and effective management policies and programs will be required to potentially reduce the rates of new invasions and identify mitigation strategies. We present the first proposed NIS research and management agenda for Chile developed through a collaborative process between researchers and the Chilean government, with a joint vision of both the challenges and solutions.