If the amygdala is involved in shaping perceptual experience when affectively significant visual items are encountered, responses in this structure should be correlated with both visual cortex responses and behavioral reports. Here, we investigated how affective significance shapes visual perception during an attentional blink paradigm combined with aversive conditioning. Behaviorally, following aversive learning, affectively significant scenes (CS(+)) were better detected than neutral (CS(-)) ones. In terms of mean brain responses, both amygdala and visual cortical responses were stronger during CS(+) relative to CS(-) trials. Increased brain responses in these regions were associated with improved behavioral performance across participants and followed a mediation-like pattern. Importantly, the mediation pattern was observed in a trial-by-trial analysis, revealing that the specific pattern of trial-by-trial variability in brain responses was closely related to single-trial behavioral performance. Furthermore, the influence of the amygdala on visual cortical responses was consistent with a mediation, although partial, via frontal brain regions. Our results thus suggest that affective significance potentially determines the fate of a visual item during competitive interactions by enhancing sensory processing through both direct and indirect paths. In so doing, the amygdala helps separate the significant from the mundane.