The recent peace process between the Colombian government and the Revolutionary Armed Forces of Colombia (FARC) has prompted radical changes in the country’s Amazon region. A decrease in violence has been accompanied by an increase in deforestation, suggesting that good things do not always come together. My dissertation studies the political economy of Amazon deforestation through a cross-disciplinary analysis linking studies of modern state formation with tropical deforestation. As such, it offers an empirically grounded explanation for differential levels of deforestation in the Colombian Amazon. Employing a mixed-methods research strategy, I reviewed historical archives on regional development, interviewed more than ninety local leaders in the region, and produced an original geodatabase on cumulative forest loss. This empirical strategy allowed me to measure Amazonian deforestation since the 1970s and systematically compare Caquetá and Putumayo, which are the two most similar departments with different levels of cumulative deforestation. Based on this research design, this dissertation suggests that an explanation of different levels of cumulative deforestation needs to seriously consider both the degree and the type of territorial integration. Cumulative deforestation and territorial integration tend to be high in departments like Caquetá and Putumayo, which transitioned from extractive economies to agrarian colonization in the first decades of the twentieth century. Both cases were economically and politically similar until the mid-1950s, when their economic and political incorporation trajectories and corresponding levels of deforestation began to diverge as a result of the different integration strategies promoted by the Colombian state between 1948 and 1982 during the ‘developmental era’. Cumulative deforestation in Caquetá (compared to Putumayo) tends to be higher because both the state and market forces succeeded in establishing an integration trajectory based on the farming of livestock. This research has the potential to improve our understanding on the geopolitical drivers of Amazon deforestation. Contemporary explanations that emphasize the withdrawal of the FARC are incomplete insofar as they fail to recognize that the guerilla organization used to be very influential in both departments and that deforestation in post-conflict Colombia has not increased equally. My dissertation also illustrates the necessity of avoiding the geographical determinism characteristic of much recent political science research and recognizing that geographical phenomena can sometimes be endogenous to the discipline’s most important variables of interest. An increasing interest in environmental issues has the potential to compel scholars and policy makers to better understand exactly how geography matters, both socially and politically.