QuEChERS CEN Standard Method EN 15662 method was used with some modification for better efficiency of the extraction and purification of pesticides residues in fruits and vegetables matrix. The extracts were analyzed by GC–MS/MS for 14 multiclass pesticides in fruits and vegetables. The method was validated with real matrix with good efficiency ranging from 73 to 124% and the LODs and LOQs were 0.001–0.4 μg kg−1 and 0.002–1.0 μg kg−1 respectively. The method was applied to investigate the level of pesticide residues in 58 fruits and vegetables and with four condition: with and without washing, with and without skin. This condition is to simulate the condition how people consume fruits and vegetables and to find out if with the sample act, the level of pesticides can be reduced. This studied confirmed the absences or lower concentration of pesticides in organic fruits and vegetables compared to which originated from intensive agricultural where pesticides are widespread used. The results were then compared to the maximum residue limits for each pesticides and in each matrix. Our results allow to conclude that washing or removing skin should be one of the solution to reduced health impact related to pesticide in fruits and vegetables.