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Abstract Event boundaries help structure the content of episodic memories by segmenting continuous experiences into discrete events. Event boundaries may also serve to preserve meaningful information within an event, thereby actively separating important memories from interfering representations imposed by past and future events. Here, we tested the hypothesis that event boundaries organize emotional memory based on changing dynamics as events unfold. We developed a novel threat-reversal learning task whereby participants encoded trial-unique exemplars from two semantic categories across three phases: preconditioning, fear acquisition, and reversal. Shock contingencies were established for one category during acquisition (CS+) and then switched to the other during reversal (CS−). Importantly, reversal either was separated by a perceptible event boundary (Experiment 1) or occurred immediately after acquisition, with no perceptible context shift (Experiment 2). In a surprise recognition memory test the next day, memory performance tracked the learning contingencies from encoding in Experiment 1, such that participants selectively recognized more threat-associated CS+ exemplars from before (retroactive) and during acquisition, but this pattern reversed toward CS− exemplars encoded during reversal. By contrast, participants with continuous encoding—without a boundary between conditioning and reversal—exhibited undifferentiated memory for exemplars from both categories encoded before acquisition and after reversal. Further analyses highlight nuanced effects of event boundaries on reversing conditioned fear, updating mnemonic generalization, and emotional biasing of temporal source memory. These findings suggest that event boundaries provide anchor points to organize memory for distinctly meaningful information, thereby adaptively structuring memory based on the content of our experiences.