The Amazon basin contains some of the most productive ecosystems on the planet, yet we have little understanding of the long-term behavior. By examining historical climate records over the Amazon, we identify several modes of climatic variability—including previously undocumented long-term modes. Furthermore, using a process-based ecosystem model, we show that these variations in climate generate variations in terrestrial carbon fluxes on short (3–4 year), intermediate (8–9 year), and long (24–28 year) time scales. The long-term cycles in terrestrial carbon balance have not been previously suggested. Finally, we find that time-lags between productivity and decomposition enhance the short-term variations in net carbon balance, while slightly dampening the long-term variations. Given the worldwide attention on terrestrial carbon cycling, and the potential for “carbon sinks”, we suggest that an improved understanding of long-term climatic and ecosystem processes is crucial. Other regions should be examined for potential long-term carbon cycle variations.