Recent research suggests that cognitive performance might be altered by the respiratory-synchronized activity generated in the brain. Previous human studies, however, have yielded inconsistent results when assessing task performance during distinct respiratory phases (inspiratory phase vs. expiratory phase). We therefore tested whether cognitive performance was regulated based on the timing of breathing components (e.g., expiratory-to-inspiratory (EI) phase transition) during the retrieval process. To determine the role of respiration in performance, the present study employed healthy subjects (n = 18) in a delayed matching-to-sample visual recognition task where a test cue was given in the respiratory phase-locked (Phased) or regularly paced (Non-phased) presentation paradigm. During the Phased session but not during the Non-phased session, the response time (RT) of the task increased by 466 ms (p = 0.003), and accuracy decreased by 21.4% (p = 0.004) when the retrieval process encompassed the EI transition. Breathing-dependent changes were particularly prominent when the EI transition occurred during the middle step of the retrieval process. Meanwhile, changes in the RT and accuracy were not observed when the retrieval process encompassed the inspiratory-to-expiratory phase transition. This is the first time that a certain phase transition in the respiratory cycle has been shown to modulate performance on a time scale of several seconds in a cognitive task. We propose that attenuation of these breathing-dependent cognitive fluctuations might be crucial for the maintenance and stability of successful performance in daily life and sports.