Ephemeral intermediates often hold the key to a more detailed understanding of chemical reaction pathways. Online methods to unambiguously identify the structure of such molecular entities, in particular in the presence of multiple isomers, are scarce. This paper presents a methodology that allows real-time monitoring of isomeric solution-phase reaction intermediates of continuous-flow reactions by coupling a microfluidic chip-reactor to a cryogenic ion trap triple mass spectrometer.