Apple peel is frequently exposed to pesticides, especially in the last stages of the pesticide treatment practice. For a certain period, peel retains most of the applied pesticides, which precisely indicates the presence of pesticide residues. This study was conducted to establish and evaluate the method for the residue analysis of pyrimethanil, cyprodinil, trifloxystrobin, bifenthrin and boscalid by GC–MS in peel of Granny Smith, Golden Delicious and Idared varieties. The method consisted of few steps, without the routine usage of sorbents, and resulted in efficient removal of waxes, targeted as main interferences in GC–MS analysis. The matrix effect, boscalid selectivity issue, trend of lower trueness for bifenthrin in all matrices and for all analytes in Granny Smith matrix were in some way associated with the waxes. Finally, the method was applied to the analysis of three varieties of apple orchard samples, after 9 and 5 months of treatment with commercial formulations that contain pyrimethanil, cyprodinil and boscalid as active ingredients. Since the developed method consisted of few steps and used nontoxic and economic reagents, it could be implemented as a fast, economic and reliable screening method.