Pesticides are chemicals used in agriculture to prevent insects, fungi, weeds, and other pests, from damaging crops. In addition, some types of pesticides are used after harvest as sprout suppressant agents help keeping the quality parameters of crops during storage. Nonetheless, its presence, even at trace levels, in food products is becoming a big challenge regarding human health. The current work aimed to develop and validate a sensitive and high-throughput analytical approach, based on a state-of-the-art microextraction technique—µQuEChERS, combined with ultra-high performance liquid chromatography equipped with a photodiode array detection system (UHPLC-PDA) to quantify isopropyl-N-(3-chlorophenyl) carbamate (chlorpropham), commonly used as efficient sprout suppressant stored potatoes, in raw and cooked potatoes cultivated in different geographical regions of Madeira Island (Portugal). Good results were obtained in terms of figures of the merit of the method, with correlation coefficients (R2) higher than 0.999 and recoveries between 94.5% to 125%. Method limit of detection (LOD) and limit of quantification (LOQ) were 0.14 μg/Kg and 0.43 μg/Kg, respectively, which are much lower than the accepted and legislated requirements by the European Union, which is 20 μg/Kg for chlorpropham. The concentration of chlorpropham in raw potatoes is significantly higher when compared to cooked samples, which revealed that the thermic treatment during cooking had a significant effect on its degradation. A significant decrease (90%, on average) was observed on chlorpropham levels.