As island ecosystems are among the most critical breeding habitats for seabirds, their protection should enhance population viability for many species. The Peruvian Diving-petrel Pelecanoides garnotii breeds only in Chile and Perú, is an endangered seabird with historically large populations of over 100,000 breeding pairs, but fewer than 1,000 remained in the 1980s and it became the first endangered seabird of the Humboldt Current System. In Chile, they breed on five islands, three of which are legally protected, but only two have a management plan. Between 2010 and 2014, we evaluated the density of nests, burrow occupancy, and colony patch sizes on the islands to estimate the breeding population. The population trend was assessed by compiling historical data available in the literature and several unpublished technical reports. The current breeding population size in Chile was ∼12,500 breeding pairs (95% CI: 10,613–14,676 pairs) that is ∼34% of the breeding pairs reported for Peru (∼36,450 pairs). Choros Island, the only island with adequate protection, accounted for ∼95% of the total breeding population of the Peruvian Diving-petrel in Chile. Historical population trends showed a significant increase in breeding pairs during recent years on Choros Island. It seems that the adequate legal protection of Choros Island is leading to the recovery of Peruvian Diving-petrels, demonstrating that protection of breeding colonies remains an essential strategy for the conservation of endemic seabirds.