The production of nutraceuticals is a growing trend, as many consumers consider them an important part of the modern active lifestyle. Others rely on the use of nutraceuticals instead of prescribing pharmaceuticals to improve their health more naturally. One of the major concerns in the nutraceutical industry is the potential presence of contaminants. Even low concentrations of contaminant residues can be harmful, so analytical methods that are sensitive at ultratrace levels are needed. Dispersive liquid–liquid microextraction method combined with fast gas chromatography and mass spectrometry was developed for the inspection of pesticide residues in Carmelite drops. The most suitable recoveries are presented when the alcohol content is fixed at 20% in Carmelite drops. The method was validated; the linearity, limits of detection/quantification, the method accuracy and precision were obtained. The complex nutraceutical matrix causes significant complications in quantitative analysis; therefore, the main target of the work was placed on studying the effects of the matrix on the correct expression of the resulting concentration of contaminants in different types of samples. An in-depth study of matrix factors was carried out, and its relationship with the content of potential interferents from the medicinal products as well as other components added during the drops’ production was discussed. Related medicinal plant-derived nutraceuticals were tested, the method was applied for real-life samples, and positive findings are herein reported.