Ecuador, a country with nearly unparalleled levels of biodiversity and endemism, has one of the highest deforestation rates of South America. I examined whether governmentally protected areas in Ecuador have been effective at reducing deforestation. After estimating deforestation rates from existing land cover change data for 2000 to 2008, I used a matching approach to compare the rates of forest loss inside and outside protected areas, which corrected for geographic biases in the locations of protected areas. I tested for the effects of protected area age, size and level of protection on the rate of deforestation using generalized linear models. Governmentally protected areas still experienced deforestation – with no apparent effect of age, size and level of protection – of nearly 10,000 ha per year, but deforestation rates were lower inside compared to outside protected areas. Governmental protection led to the avoidance of additional deforestation of 2600–7800 ha of natural forest per year. Actions to mitigate deforestation in Ecuador are of global importance and as such it is promising that protected areas can help diminish deforestation, although the effectiveness of Ecuador's protected areas can still be improved upon.