Background Stroke is the leading cause of long-term disability, making the search for successful rehabilitation treatment one of the most important public health issues. A better understanding of the neural mechanisms underlying impairment and recovery is critical for optimizing treatments. Objective: We studied the longitudinal changes in brain oscillatory modes, linked to GABAergic system activity, and determined their importance for residual upper-limb motor functions and recovery. Methods Transcranial Magnetic Stimulation (TMS) was combined with scalp Electroencephalography (EEG) to analyze TMS-induced brain oscillations in a cohort of 66 stroke patients in the acute (N = 60), early (N = 48), and late subacute stages (N = 37). Results A data-driven parallel factor analysis (PARAFAC) approach to tensor decomposition extracted brain oscillatory modes, which significantly evolved longitudinally across stroke stages (permutation tests, p Bonf < 0.05). Notably, the observed decrease of the α-mode, known to be linked with GABAergic system activity, was mainly driven by the recovering patients and was supportive of stroke recovery at the group level (Bayesian Kendall correlation, moderate to strong statistical evidence). Conclusions Overall, longitudinal evaluation of brain modes provides novel insights into functional reorganization of brain networks after a stroke. Notably, we propose that the observed α-mode decrease could correspond to a beneficial disinhibition toward the late subacute stage that fosters plasticity and facilitates recovery. These results confirm the relevance of future individual and direct monitoring of post-stroke modulations in inhibitory system activity, with the ultimate goal of designing electrophysiological biomarkers and refining therapies based on personalized neuromodulation.