Non-iridescent, structurally-based coloration in birds originates from the feather’s internal nanostructure (the keratin spongy matrix), but the presence of melanin and the characteristics of the barb’s cortex can affect the resulting color. Here we investigate how this nanostructure is regulated and combined with other elements in differently-colored plumage patches. To do so, we investigated the association between light reflectance and the morphology of feathers from the back and belly plumage patches of male Swallow Tanagers (Tersina viridis), which look greenish-blue and white, respectively. Both plumage patches have a reflectance peak around 550 nm, but the reflectance spectrum is much less saturated in the belly. The barbs of both types of feathers have similar spongy matrices at their tips which produce similar reflectance spectra. However, the color of the belly feather barbs changes from light green at the tip to white closer to the rachis. These barbs lack pigments and their morphology changes considerably: the spongy matrix is reduced, being almost hollow, and has a different shape towards the rachis. Instead, we observed deposition of melanin underneath the spongy matrix in the back feathers which had a much saturated coloration that was consistent along the barbs’ length. Overall, our results suggest that the color differences between the white and greenish-blue plumage are mostly due to the differential deposition of melanin and a reduction of the spongy matrix in some parts of the belly feather barbs, and not a result of changes in the periodicity of the spongy matrix.