Electrification of Canada’s energy and transport sectors is essential to achieve net-zero emissions by 2050 and will require a vast amount of raw materials. A large proportion of these critical raw materials are expected to be sourced from as yet undiscovered mineral deposits, which has the potential to accelerate environmental pressures on natural ecosystems. Herein we overlay new prospectivity model results for a major source of Canada’s battery minerals (i.e., magmatic Ni ± Cu ± Co ± PGE mineral systems) with five ecosystem services (i.e., freshwater resources, carbon, nature-based recreation, species at risk, climate-change refugia) and gaps in the current protected-area network to identify areas of high geological potential with lower ecological risk. New prospectivity models were trained on high-resolution geological and geophysical survey compilations using spatial cross-validation methods. The area under the curve for the receive operating characteristics (ROC) plot and the preferred gradient boosting machines model is 0.972, reducing the search space for more than 90% of deposits in the test set by 89%. Using the inflection point on the ROC plot as a threshold, we demonstrate that 16% of the most prospective model cells partially overlap with the current network of protected and other conserved areas, further reducing the search space for new critical mineral deposits. The vast majority of the remaining high prospectivity cells correspond to ecoregions with less than half of the protected areas required to meet national conservation targets. Poorly protected ecoregions with one or more of the five ecosystem services are interpreted as hotspots with the highest potential for conflicting land-use priorities in the future, including parts of southern Ontario and Québec, western Labrador, and northern Manitoba and Saskatchewan. Managing hotspots with multiple land-use priorities would necessarily involve partnerships with both Indigenous peoples whose traditional lands are affected, and other impacted communities. We suggest that prospectivity models and other machine learning methods can be used as part of natural resources management strategies to balance critical mineral development with conservation and biodiversity values.