Experiencing stress before an event can influence how that event is later remembered. In the current study, we examine how individual differences in one's physiological response to a stressor are related to changes to underlying brain states and memory performance. Specifically, we examined how changes in intrinsic amygdala connectivity relate to positive and negative memory performance as a function of stress response, defined as a change in cortisol. Twenty-five participants underwent a social stressor before an incidental emotional memory encoding task. Cortisol samples were obtained before and after the stressor to measure individual differences in stress response. Three resting state scans (pre-stressor, post-stressor/pre-encoding and post-encoding) were conducted to evaluate pre- to post-stressor and pre- to post-encoding changes to intrinsic amygdala connectivity. Analyses examined relations between greater cortisol changes and connectivity changes. Greater cortisol increases were associated with a greater decrease in prefrontal-amygdala connectivity following the stressor and a reversal in the relation between prefrontal-amygdala connectivity and negative vs. positive memory performance. Greater cortisol increases were also associated with a greater increase in amygdala connectivity with a number of posterior sensory regions following encoding. Consistent with prior findings in non-stressed individuals, pre- to post-encoding increases in amygdala-posterior connectivity were associated with greater negative relative to positive memory performance, although this was specific to lateral rather than medial posterior regions and to participants with the greatest cortisol changes. These findings suggest that stress response is associated with changes in intrinsic connectivity that have downstream effects on the valence of remembered emotional content.