Natal environment and parental quality can influence offspring phenotype, including physiological and morphological traits. We investigated how offspring morphology and feather corticosterone (CORTf; a physiological index of allostatic load) may be related to nest environment and parental characteristics by cross-fostering 3-day-old nestling Tree Swallows (Tachycineta bicolor (Vieillot, 1808)) between quaking aspen (Populus tremuloides Michx.) and plywood nest boxes that differed in microclimate. We evaluated the relative importance of natal influences, common rearing environment, and nest-box environment on nestling quality. Nestlings raised in quaking aspen boxes tended to have lower CORTf, although this result only approached significance. Nestling body mass was best predicted by the biological mother’s mass and random effects of natal and rearing nest identity, wing length was best predicted by random effects of rearing nest, and head–bill length was best predicted by random effects of natal nest. Therefore, nest microclimate was more important than maternal characteristics in predicting nestling physiology (CORTf), while nestling morphology was influenced by maternal morphology, as well as natal and rearing nest environments. Our study provides important information about how environmental and parental influences affect nestling phenotype and will help future studies interpret similar morphological and physiological indices of nestling quality.