Pesticide residue analysis in fruits and vegetables is generally performed with the QuEChERS method, when clean-up is mainly achieved with primary secondary amine (PSA) by dispersive solid phase extraction (dSPE). In this work, we present a rapid and efficient method for the clean-up of fruit and vegetable extracts with polyethyleneimine (PEI) as alternative to PSA. Clean-up of QuEChERS extracts with a mixture of branched PEI adsorbed on magnesium sulfate and silica gel was realized in 10 min, when several polar matrix components were clearly reduced. The success of the clean-up for representative matrices was visualized by both high-performance thin-layer chromatography with different detection options and total ion current chromatograms of liquid chromatography–mass spectrometry analyses. Generally, dSPE clean-up with PEI was at least equally effective as dSPE with PSA, but PEI clearly superimposed PSA in terms of adsorption capabilities towards fatty acids. After clean-up of fatty acid mixtures with 150 and 300 mg/L, total fatty acids were reduced by 98% and 99%, respectively, while PSA left two- and three-fold quantities. Additionally, the susceptibility of base-labile pesticides towards PEI as compared to PSA generally was negligible, further supporting the high suitability of PEI for clean-up in pesticide residue analysis. Thus, clean-up with PEI enables a clear reduction of various matrix compounds in fruit and vegetable extracts and provides a rapid, convenient and low-cost alternative to the existing dSPE methods with PSA.