Conservationists have long argued that inadequate funding for managing protected areas (PAs) jeopardizes their ability to achieve conservation goals. However, this claim has rarely been substantiated by quantitative evaluations. To address this, we examined the impact of funding on PA effectiveness both at the scale of 17 national PA systems across Latin America and within a PA system (Ecuador), for which we had precise historical financial data. Most PAs reduced deforestation between 2000 and 2010, demonstrating their crucial role in forest conservation. However, large deficits in funding considerably reduced the effectiveness of PAs in Ecuador (on average, a unit decrease in deficit leads to a 3.07% increase in effectiveness in avoiding deforestation). While differences in effectiveness between individual PAs in Ecuador were associated with funding deficits, national-level socioeconomic metrics (e.g., the Human Development Index) were the major factor when comparing PA system-level effectiveness among countries. This result suggests that while funding plays a major role in the performance of individual PAs, the quality of the socioeconomic context at the country level is critical for the overall performance of the PA systems. We, therefore, emphasize that maximizing the effectiveness of PAs requires a multilevel approach that includes better and more strategic resource allocation for individual PAs, combined with actions for strengthening the governance and institutions that regulate PA systems.