Ethnic differences trigger immediate implicit stereotyping, potentially influencing intergroup interactions and reinforcing social inequality. Studies indicate that ethnic biases can reduce sensorimotor resonance toward out-group members, identifying the medial prefrontal cortex (mPFC) as part of a network involved in ethnic stereotyping regulation. The specific impact of ethnic biases on individuals’ ability to coordinate actions with others and the role of mPFC in mediating in-/out-group interactions remain unclear. We investigated whether: i) interfering with mPFC activity modulates ethnic biases measured through affective misattribution procedure (AMP); ii) this interference affects coordination during a joint action task with ethnic out/in-group virtual partners. Continuous theta burst stimulation (cTBS) was used to interfere with the activity of mPFC (Experiments 1, 3) or left ventral Premotor Cortex (Experiment 2), and Vertex stimulation was included as active control site. Stimulating mPFC did not significantly affect either ethnic bias as measured through AMP nor individuals’ interaction abilities when coordinating with out-/in-group members. However, participants’ motor preparation times increased when interacting with an ethnic out-group compared to an in-group partner, regardless of the stimulation site. These findings highlight how ethnic membership influences social categorization and motor abilities during interpersonal interactions while limiting the role of mPFC in mediating inter-group motor coordination as measured in the present study.