Reproductive success of endangered Humboldt penguin (Spheniscus humboldti) colonies in Peru has been associated with nesting habitat type, presumably due to differences in environmental exposure and activity patterns that may affect energy demands and metabolism. Gas chromatography and mass spectrometry were used to determine serum concentrations of 19 saccharides from 30 Humboldt penguins nesting at Punta San Juan, Peru in order to evaluate differences in metabolic state between penguins nesting in a sheltered burrow or crevice (n = 17) and those in exposed surface nests (n = 13). Univariate and multivariate statistical analyses identified serum saccharides (arabinose, maltose, glucose-6-phosphate, and levoglucosenone in particular) that were nest-dimorphic with substantial differences between surface- and sheltered-nesting penguins. Four sugars (arabinose, xylose, fructose-6-phosphate, and sucrose) had ≥ 2-fold difference in concentration between nest types. Seven saccharides were in the top five subsets generated by discriminant analysis; four of these are simple sugars (D-glucopyranose, α ⇄ β; D-glucose; D-maltose; and D-mannose) and three are derivatives (glucose 6-phosphate, levoglucosenone, and N-acetylglucosamine). D-ribose had the highest information values (generated from weight-of-evidence values) followed by glucose 6-phosphate, levoglucosenone, and D-galactose. Sex was not a significant predictor of saccharide concentration. Levoglucosenone, which is a metabolite of the environmental contaminant levoglucosan, was significantly higher in surface-nesting penguins, reflecting a higher rate of exposure in non-sheltered penguins. Differences in the saccharide profiles of surface- and sheltered-nesting Humboldt penguins likely reflect increased metabolic requirements of surface-nesters at Punta San Juan. Conservation of appropriate sheltered-nesting habitat for penguins is essential for sustained reproductive success and colony health.