Chemical investigation of ethyl acetate bark extracts of Indigofera ammoxylum red and white phenotypes led to the bio-guided isolation of four previously undescribed flavonoids, named (2S,3R)-3′,7-dihydroxy-4′,6-dimethoxyflavanol (1), (2S,3R)-6-methoxy-7-hydroxyflavanol (2), 2′,3′,7-trihydroxy-4′,6-dimethoxyisoflavone (7) and 2′,5'-dimethoxy-4′,5,7-trihydroxyisoflavanone (8), along with 14 known compounds (3-6 and 9-18). The previously undescribed structures were characterized based on NMR, HRESIMS, UV and IR data. Published spectroscopic data were used to deduce the structure of the known compounds. Eleven of the 18 isolated metabolites were evaluated for anti-inflammatory activity and cytotoxic activity against human liver carcinoma cells and human colon and colorectal adenocarcinoma cells. All tested compounds showed an anti-inflammatory activity (IC 50 NO < 25 μg/mL), and compounds 2 and 3 were more selective than the positive control dexamethasone. Afromorsin (6) showed promising cytotoxic properties against both cancer cell lines (IC 50 18.9 and 11.4 μg/mL). Feature-based molecular networking approach applied to bark and leaves extracts of the two phenotypes allowed to detect bioactive analogues, belonging to the families of flavones, isoflavones, flavanones, flavanols and flavonols, and to explore the chemodiversity of the species. The red and white phenotypes have a similar composition, whereas bark and leaves contain specific chemical entities. Finally, this approach highlighted a cluster of potentially bioactive and undescribed metabolites.