Industrial agriculture came to dominate the entire São Tomé’s landscape during the last decades of the nineteenth century. In this Equatorial Island, part of the Portuguese African empire, planters, experts, workers, trees, and machines built cocoa plantations as concentrated spaces of modernity. By studying those ecologies, the goal of the present paper is to understand how the entangled technoscientific practices, which range from scientific agriculture and environmental management to public health, built and sustained a specific colonial regime. Such technological systems, aimed at producing the highest amount of quality cocoa at the lowest cost, depended on intensive exploitation of plants and humans. Both were perceived as machines, considered in terms of inputs and outputs. If the scientific knowledge required to make productive cocoa trees has already received academic attention, less attention has been paid to the study of medical expertise necessary to create efficient working bodies. In this paper I will show how the work of doctors was shaped and conditioned by this human built ecosystem, connecting medical knowledge and environment in a single narrative. In the highly controlled and surveyed plantations, doctors found a perfect place to adapt the agronomic practices of record keeping to humans. In an overall context of scarcity, there were quantification instruments, such as tables, charts and maps, even more than microscopes, which served as medical tools. Health issues were tackled as engineering problems, and according to the laws of political economy. Food supplies, representing the largest expenditure of the estates’ budget, became a strategic matter. In order to keep the bodies fit, but also to cope with the international criticism that surrounded São Tomé’s coercive labour regimes, plantation diets became a State affair in which experts from the Lisbon School of Tropical Medicine played a leading role. Along with food, housing and sanitation was a standard task in the work of medical practitioners. Moreover, such hygiene practices fostered, and confirmed it scientifically, the idea of morally and racial constituted diseases, defining concepts of race that fuelled European colonization in Africa.