Rationale Capsaicinoids are prevalent secondary metabolites in many natural and synthetic pharmacological compounds. To date, several soft ionization studies related to capsaicinoids have been reported; they all proposed a common fragmentation pattern based on a rearrangement of the aromatic double bonds and the fragmentation of the various positional acyl chains. However, the mechanism has never been validated by high‐resolution analyses. Consequently, in this work, a validated fragmentation mechanism of the main capsaicinoids, capsaicin (1) and dihydrocapsaicin (2), is offered. Methods In order to propose and validate a common electron ionization (EI) fragmentation mechanism for the target analytes, the following mass spectrometric methods were employed: collision‐induced dissociation (CID) by means of linked scans (LS), reinforcing the methodology by high‐resolution mass spectrometry (HRMS), in addition to appropriate deuterium‐labeled experiments performed using gas chromatography/mass spectrometry (GC/MS) and direct analysis in real time (DART). Results In a first stage, a common EI fragmentation pattern comprising two pathways was proposed for compounds 1 and 2; then, the suggested mechanism was validated by CID‐LS together with HRMS complemented by DART‐deuterium‐labeling studies. The obtained results are indicative that the corresponding molecular ions were conveniently observed, m/z 305 and m/z 307; it is worth noting that the common base peak is in correspondence with a tropylium ion derivative (m/z 137), as a consequence of a McLafferty rearrangement. In addition to these highlighted fragments, other common ions, m/z 122 and m/z 94, and their corresponding trajectory, were confirmed using the same approach. Finally, the proposed mechanism was complementarily validated by deuterium‐labeling studies, taking into account the two exchangeable hydrogens present in the phenolic and the amidic moieties. Conclusions A common validated EI fragmentation pattern for both capsaicin and dihydrocapsaicin was established using appropriated mass spectrometric methods together with convenient hydrogen/deuterium labeling. This study provides a new alternative to validate mechanisms of fragmentation of important natural products.