The apples of Red Delicious are round fruits that have red colour when ripe according to which they are named. They can be eaten fresh, but also can be processed into a variety of processed products including apple juice. In order to grow or obtain better yield of a good quality apples, pesticides are usually used to protect apple trees, but they can adversely affect human health, therefore, some precautions should be taken when these chemicals are used as food contact materials. This study summarizes the presence of chlorpyrifos pesticide residues in apples that are prepared by different methods including mechanical treatments, fresh, washed, peeled as well as heat treatment of apples when prepared into an apple juice. For this purpose, the QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) method was used for residue extraction in apple samples after different methods of preparation, and their analyses were performed by liquid chromatography-mass spectrometry (LC-MS/MS). The concentration of the pesticide chlorpyrifos in different samples of apples was in the range of less than 0.0005 mg.kg−1 to 0.00348 mg.kg−1. This study provides a conclusion that all samples of apples are safe for consumption while the peeling method and heat treatment are the most efficient in reduction of chlorpyrifos content in the final products.