This study investigated the effect of bread-making on the fate of 29 different tropane (TAs), opium (OAs), and pyrrolizidine (PAs) alkaloids. The variation in the content of these compounds was determined during the fermentation stage and subsequently after baking. Doughs were prepared with ingredients that were likely to be naturally contaminated and those analytes that were not naturally present were also added to monitor them through the process. In general, fermentation led to reductions in the content of TAs, OAs and PAs, with some exceptions. In contrast, fermentation plus baking resulted in greater variability, producing increases and decreases depending on the compounds. These findings emphasize the compound-specific and process-dependent nature of alkaloid transformations during bread-making and highlight that while the processes can reduce alkaloid levels, significant residues may persist or even increase due to interconversion, underscoring the importance of evaluating food processing effects on chemical contaminants in a compound-specific manner.