Freeze-dried fruit products are advertised as a "healthy" snack for children and adults. Strawberries, due to their water and sugar content, are prone to mold, and that is why various agrochemicals, such as pesticides, are used. During the freeze-drying process, substances with positive biological activity and possible harmful substances (e.g., pesticide residues) are concentrated and can pose a certain health risk. A total of 58 freeze-dried fruit products available on the Czech market were analyzed, including 46 samples of strawberries and 12 samples of raspberries, with some products being examined across different batches. QuEChERS extraction procedure was used for multi-residue determination of pesticide residues, followed by LC-MS/MS and GC-MS/MS analysis (and LC-MS/MS analysis of mycotoxins). QuPPe methodology was used for the extraction of polar pesticide residues followed by LC-MS/MS analysis. A total of 111 different pesticide residues (or their metabolites) and 3 mycotoxins were detected. In one of the analysed samples, more than 70 different pesticide residues were detected, of which 12 exceeded the maximum residue limit. Overall, more than 30 different residues were detected in 11 samples. Prohibited substances such as carbofuran, omethoate, and haloxyfop residues were also detected, which can pose a serious health risk. The study highlights the importance of monitoring pesticide residues in freeze-dried fruits to ensure consumer safety, especially since these products are often consumed by small children. Given the higher levels of contamination found in strawberries, it is crucial to consider the potential health risks, particularly for vulnerable groups such as young children who are more sensitive to chemical exposures.