Although the interest of the QuEChERS method has been increasing in Japan due to its simplified method, there is no information on the difference in cleanup degree between the official method for multiresidue pesticide analysis in Japan and the QuEChERS method. The purpose of this study was to compare the matrix components remaining in the sample extracts prepared using two different methods. A metabolomics technique was used to investigate the matrix components. The result showed that sugars, flavonoids, and fatty acids remained in the sample extracts using the QuEChERS method. The lack of a buffer solution and insufficient dehydration were considered as reasons for the remaining sugars and flavonoids. In the case of fatty acids, the ion exchange interaction was insufficient using dispersive SPE. Whichever preparation was used, matrices specific to the sample, such as caffeine in powdered green tea, capsaicins in chili peppers, or gingerols in ginger, remained.