Climate change is one of several drivers of recurrent outbreaks and geographical range expansion of zoonotic infectious diseases in Europe. Policy and decision-makers need tailored monitoring of climate-induced disease risk, and decision-support tools for timely early warning and impact assessment for proactive preparedness and timely responses. The abundance of open data in Europe allows the establishment of more effective, accessible, and cost-beneficial prevention and control responses. IDAlert will co-create novel policy-relevant pan-European indicators that track past, present, and future climate-induced disease risk across hazard, exposure, and vulnerability domains at the animal, human and environment interface. Indicators will be sub-national, and disaggregated through an inequality lens. We will generate tools to assess cost-benefit of climate change adaptation and mitigation measures across sectors and scales, to reveal novel policy entry points and opportunities. Surveillance, early warning and response systems will be co-created and prototyped to increase health system resilience at regional and local levels, and explicitly reduce socio-economic inequality. Indicators and tools will be co-produced through multilevel engagement, innovative methodologies, existing and new data streams and citizen science, taking advantage of intelligence generated from selected hotspots in Spain, Greece, The Netherlands, Sweden, and Bangladesh that are experiencing rapid urban transformation and heterogeneous climate-induced disease threats. For implementation, IDAlert has assembled European authorities in climate modelling, infectious disease epidemiology, social sciences, environmental economics, One Health and EcoHealth. Further, by engaging critical stakeholders from the start, IDAlert will ensure long-lasting impacts on EU climate policy, and provide new evidence and tools for the European Green Deal to strengthen population health resilience to climate change.