As agricultural waste, fruit seeds have received little attention in producing natural colorant for textile dyeing application. This work uses Eriobotrya japonica L. seed skins (EJSS) as source of natural dye for the coloration and bio-functional finishing of wool fabric. Investigation has been made to the optimal extracting conditions (such as solvent system, pH, temperature and time) and natural dye characterization (chemical components, surface morphology, and thermal stability) using UV–vis, Fourier-transform infrared spectroscopy (FT-IR), Scanning electron microscope (SEM), thermogravimetric analysis (TGA), Energy Dispersive X-rays Spectroscopy (EDS) and Differential calorimetry (DSC). Flora leaves of Chinese Tallow, Folium Artemisiae Argyi and Cinnamomum Camphora were used to produce bio-mordants in this work. Pre-mordant fabric dyeing was conducted with comparisons made between bio-mordants and traditional metal ion mordants (ferrous sulfate, potassium aluminium sulfate, and copper sulfate). Results showed that pre-mordant dyeing using EJSS natural dye can produce wool fabric with a variety of shades with enhanced color strength, color fastness, and bio-functions (such as UV protection, antioxidant and antibacterial properties). Fabric mordanted with tannin-rich bio-mordant showed the best color strength and excellent functional behavior due to the high interaction between fiber and dye molecules activated by functional groups (such as phenolic groups). The outcome of this study can provide a potential to the application of agricultural waste to the natural dyeing of textile, as well as to a value-adding green waste management.