The organic food is progressively enticing purchasers’ attention, as it is recognized to be better than the food produced by the conventional agriculture and more sustainable for the natural environment. Pesticides and their metabolites can enter the human body via food and water. In the food production, over 60 thousand chemical agents are applied, while 90% of the harmful substances are consumed. The organic production is based on the qualitative and healthy food using the natural resources in an ecologically sustainable way. The European Regulations set the maximum pesticide levels (MRLs) in the organic products, which are also regulated by The United States Department of Agriculture in their National program supported by The United States Environmental Protection Agency. It is imperative to bear in mind that in the products from the organic production, the multiple detections cannot be tolerated, i.e., that one product cannot contain more than two detected pesticide residues. In this paper, a multi-residue pesticide method has been developed to determine the pesticides in the agricultural products from the organic and conventional production. In this work, 60 pesticides were analyzed using a simple QuEChERS sample preparation procedure, followed by LC-MS/MS. The tomato, potato, apple, and carrot samples from the organic and conventional products were collected from the market and the pesticide residues assessment comparing the organic to the conventional was done.