α,β-Unsaturated carbonyls are highly reactive and described as structural alerts for genotoxicity. Ten of them (either commercially available or synthesized here by combinatorial chemistry) were first investigated throughout the chocolate-making process by solvent-assisted flavor evaporation (SAFE) coupled to GC-MS/SIM. Monitored α,β-unsaturated aldehydes were formed during chocolate production, primarily through aldol condensation of Strecker aldehydes triggered by bean roasting. Notably, levels of 2-phenylbut-2-enal (up to 399 μg·kg^–1) and 5-methyl-2-phenylhex-2-enal (up to 216 μg·kg^–1) increased up to 40-fold. Dry conching caused evaporation of α,β-unsaturated carbonyls, while wet conching partially restored or increased their levels due to cocoa butter addition. Further analyses showed that α,β-unsaturated aldehydes also occurred in most commercial sweet snacks (up to 16 μg·kg^–1), although often at lower concentrations than in roasted cocoa or derived chocolates. In the end, none of the monitored α,β-unsaturated aldehydes did raise a health concern compared to current maximum use levels (2–5 mg·kg^–1). On the other hand, much higher levels of genotoxic furan-2(5H)-one were found in crepe and cake samples (up to 4.3 mg·kg^–1).