Underutilized biowaste materials are investigated for their potential as sustainable textile colorants through an approach based on mass spectrometry, bioinformatics, and chemometrics. In this study, colorful decoctions were prepared from the outer bark of Eucalyptus deglupta and fruit peels of Syzygium samarangense, Syzygium malaccense, Diospyros discolor, and Dillenia philippinensis. Textile dyeing was performed along with liquid chromatography–mass spectrometry (LC–MS)-based untargeted metabolomics to determine the small molecules responsible for the observed colors. Global Natural Products Social Molecular Networking (GNPS) guided the annotation of black-producing proanthocyanidins in D. philippinensis and E. deglupta through complexation with FeSO4 mordant. Flavonoids from the yellow-colored D. philippinensis extracts were found to be similar to those in Terminalia catappa, a known traditional dye source. A higher intensity of epicatechin in E. deglupta produced a red-brown color in the presence of Cu2+. Furthermore, Syzygium fruit peels have poor wash-fastness in cotton fibers, but bioactive chalcone unique to S. samarangense samples may be a potential nutritional food colorant. Unsupervised PCA and supervised OPLS-DA chemometrics distinguished chemical features that affect dyeing properties beyond the observed color. These findings, along with growing data on natural dyes, could guide future research on sustainable colorants.