According to recent theorizing in social psychology, social behavior is controlled not only by reflective, but also by impulsive systems. The latter are based on associative links that may influence behavior without intent. The current study examined how prejudiced implicit associations affect physiological and automatic behavioral responses. Our native Dutch participants were immersed in a virtual environment in which they encountered virtual persons (avatars) with either White or Moroccan facial features. In line with our predictions, participants maintained more distance and showed an increase in skin conductance level when approaching Moroccan avatars as opposed to White avatars. Participants’ implicit negative associations with Moroccans moderated both effects. Moreover, evidence was found that the relation between implicit prejudice and distance effects was fully mediated by skin conductance level effects. These data demonstrate how prejudiced implicit associations may unintentionally lead to impulsive discriminatory responses.