Understanding the electrochemical reaction mechanisms of energy conversion and storage systems is essential for improving their performance. Nuclear magnetic resonance (NMR) spectroscopy is excellent for probing electrochemical reactions due to its capability to provide quantitative and qualitative information. For the in situ simultaneous acquisition of the anode and cathode exhaust spectra of a direct methanol fuel cell, real-time flow-NMR spectroscopy using a toroid cavity detector was developed in our laboratory. In the cathode exhaust, the CD3OH from the anode as well as HOD was observed. Ex situ NMR spectroscopy cannot detect gas products because they are lost during sample preparation. On the other hand, the amount of CO2 gas detected in the anode exhaust using our in situ detection method was proportional to the HOD amount. It was also proportional to the cell current generated. This explains differences in the fuel cell performance by identifying generated and consumed chemicals and their pathways in the cells at respective conditions. Our results show that this in situ real-time analysis could identify and quantify the exhaust components, including the gaseous products. Therefore, our results demonstrate that this in situ real-time analysis is appropriate to study the reaction mechanisms of diverse other liquid-flowing chemical systems in addition to fuel cells. Furthermore, it may be applicable to designing advanced materials.