Despite the extensive use of flavoring substances in food, their monitoring for regulatory purposes is currently limited. This raises public health issues, especially as some compounds are prohibited due to (geno)toxicity. A solvent-assisted flavor evaporation (SAFE) method coupled with GC/MS (SIM) was validated here for diverse water-based beverages. Thirty flavoring substances out of the 38 targeted were validated, showing good analytical performances and confirming the versatility of the SAFE technique. The method was then applied to 94 samples, including fruit juices, iced teas, lemonades, colas, and sports beverages. Overall, seven different flavoring substances of interest were detected in the samples. Perillaldehyde and furan-2(5H)-one, two genotoxic flavoring substances, were found at concentrations up to 153 and 143 μg·kg^–1, respectively. Perillaldehyde levels were significantly higher in commercial citrus juices than in freshly squeezed juices. Food control laboratories could use the developed method to face the current growing need to improve flavoring substance monitoring and conduct risk assessments.