An easy and convenient procedure is described for monitoring chemical reactions and characterization of compounds dissolved in ionic liquids using the well-known tandem mass spectrometry (MS/MS) technique. Generation of wastes was avoided by utilizing an easy procedure for analysis of ionic liquid systems without preliminary isolation and purification. The described procedure also decreased the risk of plausible contamination and damage of the ESI-MS hardware and increased sensitivity and accuracy of the measurements. ESI-MS detection in MS/MS mode was shown to be efficient in ionic liquids systems for structural and mechanistic studies, which are rather difficult otherwise. The developed ESI-MS/MS approach was applied to study samples corresponding to peptide systems in ionic liquids and to platform chemical directed biomass conversion in ionic liquids.