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Commodity prices, exchange rate, infrastructural projects and migration patterns are known and important drivers of Amazon deforestation, but cannot solely explain the high rates observed in 1995 and 2003–2004 in six Brazilian Amazon states. Deforestation predictions using those widely applied drivers can underestimate deforestation rates by as much as 50%. We show that years with the highest deforestation rates also correlate with large administrative shifts caused by presidential elections which results in periods of managerial instability associated with episodic inefficiency, leading to weak institutions unable to properly combat illegal deforestation. Although surveillance and regulatory action plans to combat deforestation have held back deforestation in the Brazilian Amazon since 2005, our results suggest that environmental management institutions should be aware such administration shifts set a burden on the policy targets associated with conservation policies. Institutional vulnerability immediately after major elections is an acknowledged fact in Brazil, though it has been mostly disregarded as an indicator of ecological threat.