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The rapid worldwide increase in resource extraction is evident in Madagascar—a global biodiversity hotspot. This study examines the localized effects of operational and planned large-scale extractive investments on social-ecological systems in Madagascar and links them to the Sustainable Development Goals. The focus is on sites owned or explored by foreign investors, specifically Ambatovy Moramanga, Ambatovy Tamatave, QIT Madagascar Minerals/Rio Tinto, Ranobe, and Tantalum Rare Earth Malagasy. Employing a counterfactual approach, we gathered survey responses from 459 small-scale farming, agro-pastoral, and artisanal-fisheries-based households. The survey provided information on general household characteristics, land use, land management, livelihoods, well-being, and any perceived changes to these variables, as well as any perceived mining impacts related to the changes. Overall, respondents reported predominantly negative effects on land (and sea) use, livelihoods, well-being, and security. Mining pollution, primarily from operational sites, had reduced access to water and fisheries resources, and natural forest areas had diminished. Reduced productivity due to pollution of soils, water, and air had a negative impact on various land uses and affected people's health, particularly in the surroundings of QIT Madagascar Minerals/Rio Tinto. Although some projects, such as Ambatovy, had eventually improved healthcare and infrastructure, most negative mining impacts had occurred during both the exploratory and the operational phases of the projects. Overall, this study offers a comprehensive view of how large-scale extractive investments affect land (and sea) use and human well-being. In addition, we highlight policy implications that must be considered if large-scale extractive investments are to support progress on the 2030 Agenda.