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Synopsis We argue that the current environmental changes stressing the Earth’s biological systems urgently require study from an integrated perspective to reveal unexpected, cross-scale interactions, particularly between microbes and macroscale phenomena. Such interactions are the basis of a mechanistic understanding of the important connections between deforestation and emerging infectious disease, feedback between ecosystem disturbance and the gut microbiome, and the cross-scale effects of environmental pollutants. These kinds of questions can be answered with existing techniques and data, but a concerted effort is necessary to better coordinate studies and data sets from different disciplines to fully leverage their potential. 

Abstract Zoonotic diseases represent 75% of emerging infectious diseases worldwide, and their emergence is mainly attributed to human‐driven changes in landscapes. Land use change, especially the conversion of natural areas to agricultural use, has the potential to impact hosts and vector dynamics, affecting pathogen transmission risk. While these links are becoming better understood, very few studies have investigated the opposite question—how native vegetation restoration affects zoonotic disease outbreaks.We reviewed the existing evidence linking native vegetation restoration with zoonotic transmission risk, identified knowledge gaps, and, by focusing on tropical areas, proposed forest restoration strategies that could help in limiting the spread of zoonotic diseases.We identified a large gap in information on the effects of native vegetation restoration on zoonotic diseases, especially within tropical regions. In addition, the few studies that exist do not consider environmental aspects that can affect the outcomes of restoration on disease risk, such as the land use history and landscape structural characteristics (as composition and configuration of native habitats). Our conceptual framework raises two important points: (1) the effects of forest restoration may depend on the context of the existing landscape, especially the percentage of native vegetation existing at the beginning of the restoration; and (2) these effects will also be dependent on the spatial arrangement of the restored area within the existing landscape. Furthermore, we propose important topics to be studied in the coming years to integrate zoonotic disease risk as a criterion in restoration planning.Synthesis and application. Our results contribute to a more comprehensive forest restoration planning, comprising multiple ecosystem services and resulting in healthier landscapes for both people and nature. Our framework could be integrated into the post‐2020 global biodiversity framework targets.