The direct observation of real time electrochemical processes is of great importance for fundamental research on battery materials. Here, we use electron paramagnetic resonance (EPR) spectroscopy to monitor the electrochemical reaction of sodium ions with few-layer MoS2 and its composite with carbon nanotubes (CNTs), thereby uncovering new details of the reaction mechanism. We propose that the sodiation reaction takes place initially in structural defects at the MoS2 surface that have been created during the synthetic process (ultrasonic exfoliation), leading to a decrease in the density of Mo5+ at low symmetry sites that can be related to the electrochemical irreversibility of the process. In the case of the few-layer MoS2/CNTs composite, we found metallic-type conduction behavior for the electrons associated with the Mo paramagnetic centers and improved electrochemical reversibility. The reversible nature of the EPR spectra implies that adsorption/desorption of Na+ ions occurs on the Mo5+ defects, or that they are neutralized during sodiation and subsequently created upon Na+ extraction. These effects help us to understand the higher capacities obtained in the exfoliated samples, as the sum of electrosorption of ions and faradaic effects, and support the suggestion of a different reaction mechanism in the few-layer chalcogenide, which is not exclusively an insertion process.