An analytical method based on a modified QuPPe (quick polar pesticide) extraction procedure coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was evaluated for the determination of four polar compounds (chlorate, fosetyl-Al, maleic hydrazide, and perchlorate) in nutraceutical products obtained from soy. Experimental con- ditions including extraction such as solvent, acidification, time, and clean-up sorbents were varied. Acidified acetonitrile (1 % formic acid, v/v) was used as extraction solvent instead of methanol (conventional QuPPe), which provides a doughy mixture which cannot be injected into the LC. Clean-up or derivatization steps were avoided. For analysis, several sta- tionary phases were evaluated and Hypercarb (porous graphit- ic carbon) provided the best results. The optimized method was validated and recoveries ranged between 46 and 119 %, and correction factors can be used for quantification purposes bearing in mind that inter-day precision was equal to or lower than 17 %. Limits of quantification (LOQs) ranged from 4 to 100 μg kg^−1. Soy-based nutraceutical products were analyzed and chlorate was detected in five samples at concentrations between 63 and 1642 μg kg^−1.