The purpose of this study is to investigate the dyeing properties and the functionalities of the cotton and silk fabrics dyed with Alnus japonica bark and heartwood extracts. The dyeing properties of the fabrics were studied by investigating the characteristics of the colorants; the effect of dyeing conditions such as dye concentrations, dyeing temperatures, and the duration of dye uptakes; the effect of mordants; and color changes. The study also estimated the colorfastness, antimicrobial abilities, ultraviolet-cut abilities, and deodorant abilities of the dyed fabrics. In the ultraviolet-visible spectrum, the wavelengths of maximum absorption for the Alnus japonica bark and heartwood extracts were found to be 279 and 281 nm, respectively, and tannin was found to be the major colorant component. On the basis of Fourier transform infrared spectroscopy (FT-IR) results, tannin was assumed to be hydrolyzable. The dye uptake of silk was better than that of cotton and increased depending on the increasing dye concentration, dyeing time, and dyeing temperature. It showed relatively better affinity toward heartwood than the bark. The dyed fabric without a mordant produced a tan color and showed various other colors depending on the mordant types. The washing fastness was found to be not good, but the light, dry cleaning, and perspiration fastness were moderate. However, the rubbing fastness showed a relatively good grade. The ultraviolet-cut abilities and deodorant abilities of the dyed fabrics were improved. Moreover, the dyed fabrics showed very good antimicrobial abilities of 99.9% against Staphylococcus aureus and Klebsiella pneumoniae.