Social threat is both a source and consequence of implicit bias against Asian Americans, who are often stereotyped as “perpetual foreigners,” posing some threat to (white) American values. The implicit nature of these attitudes makes investigating anti-Asian bias difficult as self-report and behavioral data suffer from social desirability and learning effects. To investigate implicit social threat in anti-Asian bias, we presented participants with a passage critical of American values, purportedly written by a white American (ingroup) or by an Asian American author (outgroup). We utilized electrodermal responses (GSR) to measure autonomic arousal, and cerebral blood oxygenation (fNIRS) to measure cognitive control. Our results suggest that implicit social threats are physiologically represented similar to other feelings of threat, which become more extreme when interacting with a perceived outgroup member. Follow-up analyses suggest that the autonomic responses are moderated by higher-order cognitions, evidenced by changes in blood oxygenation in the anterior and dorsolateral prefrontal cortex, which occurred independently of behavioral responses obtained after the experimental manipulation. Together, these results indicate that while more abstract feelings of threat are implicitly represented in a salient physiological manner, higher-order cognitive faculties can attenuate them, and innate attitudes need not supersede mindful and learned behavior.