Herein we report the first application of infrared multiple‐photon dissociation (IRMPD) spectroscopy to study noncovalent interactions in organocatalysis. Phenylalanine‐derived iminium ions, central to numerous organocatalytic processes, display dynamic conformational behavior as a consequence of stabilizing noncovalent interactions (e.g., CH–π, π–π). Electronic modulation of the aryl ring causes notable variation in the conformation; this can be detected spectroscopically and correlated with enantioselectivity. Given that these interactions, which orchestrate stereoinduction, encode for specific conformers (I, II, or III), a diagnostic IRMPD spectrum is generated: the C=O stretching frequency of the imidazole carbonyl group serves as a diagnostic marker. The calculated conformers and their respective spectra can be compared with experimental data. Consequently, valuable insight into the ubiquitous noncovalent interactions associated with MacMillan‐catalyst‐derived α,β‐unsaturated iminium ions can be obtained in the absence of solvent or counterion effects. A preliminary structure–catalysis correlation is disclosed, thus demonstrating the potential of this approach for studying reactive intermediates and facilitating catalyst design.