Apple and apple derivatives (e.g., juices, puree) are the most important foodstuffs contaminated with patulin (PAT) in the human diet. To routinely monitor these foodstuffs and ensure that the PAT levels are below the maximum permitted levels, a method using liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) has been developed. Afterwards, the method was successfully validated, reaching quantification limits of 1.2 μg/L for apple juice and cider, and 2.1 μg/kg for puree. Recovery experiments were performed with samples fortified with PAT in the range of 25–75 μg/L for juice/cider and 25–75 μg/kg for puree. The results show overall average recovery rates of 85% (RSDr= 13.1%) and 86% (RSDr= 2.6%) with maximum extended uncertainty (Umax, k = 2) of 34 and 35% for apple juice/cider and puree, respectively. Next, the validated method was applied to 103 juices, 42 purees and 10 ciders purchased on the Belgian market in 2021. PAT was not found in the cider samples, but it was present in 54.4% of the tested apple juices (up to 191.1 μg/L) and 7.1% of the puree samples (up to 35.9 μg/kg). When comparing the results to the maximum levels set by Regulation EC n° 1881/2006 (i.e., 50 μg/L for juices and 25 μg/kg for puree for adults, and 10 μg/kg for infants and young children), exceedances were observed in five apple juices and one puree sample, for infants and young children. Using these data, a potential risk assessment for consumers can be suggested, and it is found that the quality of apple juices and purees sold in Belgium needs further regular surveillance.