In birds, energy supply during growth is a major predictor of the fledglings’ physical condition and survival prospects. Differential quantity and quality of fledglings produced under varying nestling food supplies are likely to affect the number of offspring that recruit into the breeding population. However, the underlying mechanisms and associated consequences are still poorly known. Using a partial cross-fostering and food supplementation experiment, we estimated the effect of variation in food supply during growth on nestling survival and fledgling phenotypic traits of Little Owls Athene noctua. Survival to fledging was much higher in food-supplemented nestlings (98.6%) than in control nestlings (82.4%). Furthermore, supplemented nestlings were on average 8.9 g heavier and were more likely to develop subcutaneous fat deposits (99.4 vs. 73.7% of treatment and control nestlings, respectively). Supplemented nestlings also had on average longer wings than control nestlings, but tarsi and culmen did not differ significantly. Furthermore, experimentally supplemented fledglings struggled more when handled and emerged sooner from tonic immobility than control fledglings. The irises of supplemented fledglings were less intensely coloured. The experimentally induced changes in nestling development probably affect individual performance beyond fledging. Nestlings from orchard-dominated habitats were larger than those from habitats dominated by arable land. As nestling food supply is largely determined by natural food availability, we conclude that habitat quality affects Little Owl productivity and offspring quality, and ultimately, population dynamics.