Green coffee (Coffee arabica and Coffee robusta) is one of the most commonly traded goods globally. Their beans are enriched with polyphenols and numerous health benefits are associated with their consumption. The main aim of this work was to develop a new and fast analytical HPLC-MS/MS method to simultaneously determine six flavonoid polyphenolic compounds (quercetin, rutin, isorhamnetin, quercetin-3-glucouronide, hyperoside, and quercitrin) in 22 green coffee samples from six different geographical origins (Ethiopia, Brazil, Guatemala, Nicaragua, India and Colombia). In addition, by adjusting pH, temperature, solvent type, and extraction duration, several extraction methods such as acidic and alkaline hydrolysis, and extraction without hydrolysis were evaluated. The optimal extraction procedure in terms of recovery percentages (78.67–94.09%)was acidic hydrolysis at pH 2, extraction temperature of 60 °C, extraction solvent of 70% ethanol, and extraction duration of 1.5 h. Hyperoside (878–75 μg/kg) was the most abundant compound followed by quercitrin (408–38 μg/kg), quercetin (300–36 μg/kg), rutin (238–21 μg/kg), and quercetin-3-glucouronide (225–7 μg/kg), while isorhamnetin (34–3 μg/kg) showed the lowest amount. Overall, green coffee beans are rich in flavonoid polyphenolic compounds and could be used as part of a healthy diet.