Inhibitory control relies on coordinated beta-band activity within a fronto-basal ganglia network, which implements inhibition via downstream effects on (pre)motor areas. In this study, we employed dual-site transcranial alternating current stimulation (tACS) targeting the right inferior frontal gyrus (rIFG) and primary motor cortex (M1) to directly manipulate phase relationships in the beta band and assess their effects on both functional connectivity and motor inhibition. Fifty-two healthy participants received in-phase, anti-phase and sham stimulation while performing a stop-signal task. The results revealed that connectivity between rIFG and lM1 increased following in-phase but decreased after anti-phase stimulation. Although no direct modulation of task performance was observed, the greater connectivity increase between the targets during in-phase stimulation was predictive of faster inhibitory performance. In contrast, greater connectivity decreases during anti-phase stimulation were related to faster go responses, suggesting a shift towards less inhibition on the motor system. These findings provide evidence that dual-site beta-tACS can both enhance and impair inhibitory control depending on phase alignment, highlighting its potential as a non-invasive intervention for disorders marked by impaired inhibition.