Bats are excellent ecological indicators because they are long-lived, globally distributed, and show predictable responses to environmental stressors. Unaltered bat guano deposits, although rare, can serve as environmental archives to reveal changes in dietary patterns over millennial time scales. We inferred changes in agricultural and industrial practices using a continuous 4300-year-old bat guano deposit from Jamaica. Cadmium, mercury, lead, and zinc increased during the Industrial Revolution, (which began in ca. 1760), a period characterized by elevated emissions of metals to the atmosphere. Beginning in the early 20th century, decreases in 206Pb/207Pb isotopes tracked the history of leaded gasoline use. Metal concentrations in the bat guano deposit exceeded those recorded in two nearby lake sediment cores from Jamaica. Carbon, nitrogen, and sulfur stable isotope profiles in bat guano tracked the agricultural history of Jamaica, specifically the introduction of nitrogen fertilizers, sugarcane, and possibly fungicides. Bat populations are under stress globally, and such intact guano deposits provide potentially critical information on long-term changes in their food source and exposure to metals.