Natural resource extraction projects are often accompanied by complex environmental and social-ecological changes. In this paper, we evaluated the association between commodity extraction and the incidence of diseases. We retrieved council (district)-level outpatient data from all public and private health facilities from the District Health Information System (DHIS2). We combined this information with population data from the 2012 national population census and a geocoded list of resource extraction projects from the Geological Survey of Tanzania (GST). We used Poisson regression with random effects and cluster-robust standard errors to estimate the district-level associations between the presence of three types of commodity extraction (metals, gemstone, and construction materials) and the total number of patients in each disease category in each year. Metal extraction was associated with reduced incidence of several diseases, including chronic diseases (IRR = 0.61, CI: 0.47–0.80), mental health disorders (IRR = 0.66, CI: 0.47–0.92), and undernutrition (IRR = 0.69, CI: 0.55–0.88). Extraction of construction materials was associated with an increased incidence of chronic diseases (IRR = 1.47, CI: 1.15–1.87). This study found that the presence of natural resources commodity extraction is significantly associated with changes in disease-specific patient volumes reported in Tanzania’s DHIS2. These associations differed substantially between commodities, with the most protective effects shown from metal extraction.