Stress engendered by stereotype threatening situations may facilitate encoding of negative, stereotype confirming feedback received during a performance among women in science, technology, engineering and mathematics (STEM). It is unclear, however, whether this process is comprised of the same neurophysiological mechanisms evident in any emotional memory encoding context, or if this encoding bias directly undermines positive self-perceptions in the stigmatized domain. A total of 160 men and women completed a math test that provided veridical positive and negative feedback, a memory test for feedback, and math self-enhancing and valuing measures in a stereotype threatening or neutral context while continuous electroencephalography activity and startle probe responses to positive and negative feedback was recorded. Indexing amygdala activity to feedback via startle responses and emotional memory network connectivity elicited during accurate recognition of positive and negative feedback via graph analyses, only stereotype threatened women encoded negative feedback better when they exhibited increased amygdala activity and emotional memory network connectivity in response to said feedback. Emotional memory biases, in turn, predicted decreases in women’s self-enhancing, math valuing and performance. Findings provide an emotional memory encoding-based mechanism for well-established findings indicating that women have more negative math self-perceptions compared with men regardless of actual performance.