Whether melanin-based colors honestly signal a bird’s condition during the growth of feathers is controversial, and it is unclear if, or how, the physiological processes underlying melanogenesis or the role of the microstructure of feathers in imparting structural color to feathers may be adversely affected by condition. Here, we report results from two experiments designed to measure the effect of condition on expression of eumelanic and pheomelanic coloration in black-capped chickadees (Poecile atricapillus) and zebra finches (Taeniopygia guttata), respectively. In chickadees, we compared feathers of birds affected and unaffected by avian keratin disorder, whereas in zebra finches we compared feathers of controls with feathers of those subjected to an unpredictable food supply during development. In both cases, we found that control birds had brighter feathers (higher total reflectance) and more barbules, but similar densities of melanosomes. In addition, the microstructure of the feathers explained variation in color more strongly than did melanosome density. Together, these results suggest that melanin-based coloration may in part be condition-dependent, but that this may be driven by changes in keratin and feather development, rather than melanogenesis itself. Researchers should be cautious when assigning variation in melanin-based color to melanin alone and microstructure of the feather should be taken into account.