Research on deception focused on the neurophysiological assessment of the deceiver, showing activation of specific brain areas and increased autonomic activity. However, deception is an interpersonal process where both the deceiver and the deceived interact in a constant process of evaluation that requires demanding cognitive resources. The present study aimed to investigate inter-brain synchronization (IBS) and heartbeats synchrony between an interviewer intent on detecting deception and an interviewee during a deception (Deception Group; “DG”) or truth-telling (Non-Deception Group; “NDG”) task using an ecological mock crime experiment. The results showed that DG exhibited higher IBS before the interview in the theta band and during the interview in the alpha band while displaying decreased heartbeats synchrony across all experimental phases compared to NDG. The greater IBS in DG involved particularly the left temporal area of the interviewee. These findings highlight the relevance of studying deception according to a two-person neuroscience perspective, suggesting that while neural processes are synchronized before and during a deceptive interaction, autonomic processes follow different activation patterns. Integrating the hyperscanning techniques with existing lie-detection methods could enhance the identification of neurophysiological markers of deception.