Elucidating the mechanisms by which honey bees process pollen vs. protein supplements are important in the generation of artificial diets needed to sustain managed honeybees. We measured the effects of diet on protein concentration, hypopharyngeal gland development and virus titers in worker honey bees fed either pollen, a protein supplement (MegaBee), or a protein-free diet of sugar syrup. Workers consumed more pollen than protein supplement, but protein amounts and size of hypopharyngeal gland acini did not differ between the two feeding treatments. Bees fed sugar syrup alone had lower protein concentrations and smaller hypopharyngeal glands compared with the other feeding treatments especially as the bees aged. Deformed wing virus was detected in workers at the start of a trial. The virus concentrations increased as bees aged and were highest in those fed sugar syrup and lowest in bees fed pollen. Overall results suggest a connection between diet, protein levels and immune response and indicate that colony losses might be reduced by alleviating protein stress through supplemental feeding.