Currently, most food waste is used as animal feed and this process does not take advantage of the available chemical composition. A Brazilian example is the citrus fruit processing wastes (CFPW), which have begun to draw attention due to their biological importance. In order to access the main compounds of this matrix, an efficient and environmentally friendly procedure was tested. From this extract, flavonoids as naringenin, hesperitin, chrysoeriol, sinensetin, 3,5,6,7,3',4'-hexamethoxyflavone, nobiletin, 5-methoxysalvigenin, 3,5,6,7,8,3',4'-heptamethoxyflavone, 3,5,6,7,4'-pentamethoxyflavone and isosakuranetin were identified by high performance liquid chromatography (HPLC-UV), liquid chromatography-mass spectrometry (LC-MS) and liquid chromatography-nuclear magnetic resonance (LC-NMR). This study describes the potential use of citrus waste as a source of biologically active compounds. The extraction method proposed for this work was not expensive and the flavonoids were obtained in large amounts, thus, this extraction method is being developed using pilot plant scale-up techniques and will soon be available to the industry at a low cost.