Electron ionization mass spectrometry (EIMS) combined with (electro)chemical reactions has been widely applied to various fields for the fast detection and measurement of unknown intermediates and products. This provides valuable information for further analyses of reaction mechanisms and kinetics. However, we have found chemical ionization (Chem-I) can be inadvertently involved in the EI process, and thus scramble the mass spectra, which can potentially mislead further data interpretation and analyses. The presented Chem-I scrambling phenomena is a general issue that occurs in (electro)chemistry-mass spectrometry systems, as well as gas/liquid chromatography-mass spectrometry tandem systems.