An automated method using solid-phase extraction (SPE) for the concentration and clean-up of soy isoflavone extracts is proposed in this work. Using a standardized sample (0.1 g of a freeze dried soybean extract/25 mL of water); eight SPE cartridges with a wide range of sorbents (C18, divinylbenzene and modified divinylbenzene) from different suppliers were evaluated and compared. A large variation on SPE cartridges performance was observed, especially regarding retention and breakthrough volume of isoflavones during sample load and washing steps. The most effective cartridges were the divinylbenzene based cartridges, especially Strata X (from Phenomenex) and HLB oasis (from Waters). Using Strata X cartridges, several extraction parameters, such as sample loading flow (5-15 mL min(-1)), extracting solvent volume (2-6 mL of methanol), pH of the extracting solvent and the necessity of drying the sorbent before elution, were evaluated to provide a fast, specific, quantitative and reproducible SPE method. The optimized method consists of conditioning the cartridge with 10 mL of methanol and 10 mL of water (10 mL min(-1)), loading 25 mL of the standardized extract onto the cartridges (5 mL min(-1)), washing the cartridge with 10 mL of water (10 mL min(-1)) and finally eluting with 4 mL of methanol (10 mL min(-1)). Mean isoflavones recovery was 99.37% and mean intra- and inter-day reproducibility was higher than 98%. The developed sample clean-up/concentration (6.25:1) method takes less than 10 min and can be used in the analysis of isoflavones from soy extracts.