While differences in foraging and reproductive success are well studied between seabird colonies, they are less understood at a smaller subcolony scale. Working with little penguins (Eudyptula minor) at Phillip Island, Australia, we used an automated penguin monitoring system and performed regular nest checks at two subcolonies situated 2 km apart during the 2015/2016 breeding seasons. We examined whether foraging and reproductive success differed between subcolonies. We used satellite data to examine how sea surface temperature, as environmental pressure, in the foraging regions from each subcolony influenced their foraging performance. In the pre-laying and incubation breeding stages, the birds from one subcolony had a lower foraging success than birds from the other. However, this pattern was reversed between the subcolonies in the guard and post-guard stages. Breeding success data from the two subcolonies from 2004–2018 showed that reproductive success and mean egg-laying had a negative relationship with sea surface temperature. We highlighted that variation in foraging and reproductive success can arise in subcolonies, likely due to different responses to environmental conditions and prey availability. Differences at the subcolony level can help refine, develop and improve appropriate species management plans for conserving a range of colonial central place seabirds.