Weed suppressive potential of annual pasture legumes has been previously described, the mechanism of interference with weeds has not been clearly elucidated. We, therefore, aimed to delineate the role of secondary metabolites synthesized and released by pasture legumes through a series of studies to: 1) characterize key metabolites present in plant tissues, residue and the rhizosphere and 2) correlate their presence with weed suppressive properties. Methods: Field and in vitro experimentations coupled with targeted and non-targeted metabolic profiling was performed to evaluate the abundance of key phytotoxic metabolites using UHPLC QTOF-MS. Further, those metabolites strongly correlated with weed suppression and phytotoxicity were predicted by chemometric analyses and their concentration evaluated in field soils collected from the same legume site. Results: Field experimentation, methanolic extracts and dried residues of Biserrula pelecinus L. and Ornithopus compressus L. exhibited marked phytotoxicity in a series of laboratory experiments. Metabolic profiling revealed that both foliar tissues and rhizosphere soils of pasture legumes possessed a high abundance of flavonoids and their precursors. Chemometric analyses suggested the strong association of quercetin, isoquercetin, kaempferol, and kaempferol-7-O-glucoside with weed suppression under field conditions. Specifically, the abundance of quercetin and kaempferol was significantly higher in soils collected from established stands of biserrula and yellow serradella in contrast to arrowleaf, gland and subterranean clover. Conclusion: Current study provided an evidence for the role of certain annual legume-produced flavonoids in weed suppression in southern Australia and further insight into their localization and release in the soil rhizosphere.