Theory and observations suggest that offspring abandonment in animals may occur when the costs to future reproductive output of current reproductive effort outweigh the fitness benefits of rearing the current brood. While hormonal cues (i.e. corticosterone) or energy reserves are believed to be involved, few studies have directly focused on the proximate cues influencing behaviours directly related to reproductive success. To address this information gap, we determined the incubation metabolic rates and corticosterone (CORT) levels of naturally fasting and freely incubating ancient murrelets (Synthliboramphus antiquus). Respiratory quotient (RQ) increased with date, suggesting that incubating ancient murrelets shifted from strictly lipid-based metabolism towards more protein-based metabolism as incubation progressed. Birds that hatched only one nestling had higher levels of circulating CORT than those which hatched two, suggesting that birds which laid only a single egg found incubation more stressful than those which laid two. However, CORT levels and incubation shift lengths were not correlated, suggesting that birds that undertook prolonged incubation shifts did so only when their energy stores were not jeopardized.