Establishing protected natural areas (PNA) has been one of the main policy mechanisms used for protecting flora and fauna species. However, in the last 18 years we have seen a sharp reduction in forest cover in Peru and this may have been exacerbated by the development of road infrastructure. Despite the accepted fact that roads can bring about socioeconomic benefits, it can also have negative environmental effects, such as deforestation. Using a difference in difference model with two treatments, we study the effectiveness of PNA to prevent deforestation in the presence of road infrastructure over panel data information. Our findings suggest that the expansion of the road network over the last decade has had an impact, increasing the rate of deforestation in the Peruvian Amazon. However, the increase in protected areas has partially neutralized this effect. On average, the approach of roads to within 10 km of the forests has been associated with reductions in forest coverage of around 7.1 km per 400 km2. In spite of this, the simultaneous creation of protected areas has led to a reduction in the deforestation rate of around 6.5 km2 per 400 km2. It seems that regardless of the “deforestation” effect of roads, PNA fulfill their protective role.