We examined the reproductive consequences of differential nest site use in Fork-tailed Storm-Petrels (Oceanodroma furcata) in the Aleutian Islands, Alaska, where birds on islands where foxes were introduced nest in rocky substrate rather than in typical soil habitat. We investigated how physical and microclimatic nest site characteristics influenced storm-petrel breeding success 20 years after fox removal. We then examined whether those nest site characteristics that affected success were related to the amount of rock that composed the nest. In both years of our study, nest temperature had the strongest influence on chick survival and overall reproductive success, appearing in all the top models and alone explaining 14–35% of the variation in chick survival. The relationship between reproductive success and nest temperature was positive in both years, with higher survival in warmer nests. In turn, the best predictor of nest temperature was the amount of rock that composed the site. Rockier nests had colder average temperatures, which were driven by lower daily minimum temperatures, compared to nests with more soil. Thus, the rockiness of the nest site appeared to affect chick survival and overall reproductive success through its influence on nest temperature. This study suggests that the use of rocky nest sites, presumed to be a result of historic predation from introduced foxes, could decrease breeding success in this recovering population, and thus be a long-lasting effect of introduced predators.