A novel multimodal experimental setup and dyadic study protocol were designed to investigate the neurophysiological underpinnings of joint action through the synchronous acquisition of EEG, ECG, EMG, respiration and kinematic data from two individuals engaged in ecologic and naturalistic cooperative and competitive joint actions involving face-to-face real-time and real-space coordinated full body movements. Such studies are still missing because of difficulties encountered in recording reliable neurophysiological signals during gross body movements, in synchronizing multiple devices, and in defining suitable study protocols. The multimodal experimental setup includes the synchronous recording of EEG, ECG, EMG, respiration and kinematic signals of both individuals via two EEG amplifiers and a motion capture system that are synchronized via a single-board microcomputer and custom Python scripts. EEG is recorded using new dry sports electrode caps. The novel study protocol is designed to best exploit the multimodal data acquisitions. Table tennis is the dyadic motor task: it allows naturalistic and face-to-face interpersonal interactions, free in-time and in-space full body movement coordination, cooperative and competitive joint actions, and two task difficulty levels to mimic changing external conditions. Recording conditions—including minimum table tennis rally duration, sampling rate of kinematic data, total duration of neurophysiological recordings—were defined according to the requirements of a multilevel analytical approach including a neural level (hyperbrain functional connectivity, Graph Theoretical measures and Microstate analysis), a cognitive-behavioral level (integrated analysis of neural and kinematic data), and a social level (extending Network Physiology to neurophysiological data recorded from two interacting individuals). Four practical tests for table tennis skills were defined to select the study population, permitting to skill-match the dyad members and to form two groups of higher and lower skilled dyads to explore the influence of skill level on joint action performance. Psychometric instruments are included to assess personality traits and support interpretation of results. Studying joint action with our proposed protocol can advance the understanding of the neurophysiological mechanisms sustaining daily life joint actions and could help defining systems to predict cooperative or competitive behaviors before being overtly expressed, particularly useful in real-life contexts where social behavior is a main feature.