Mindful breathing has gained considerable attention as a school-based strategy to enhance learning and well-being in students. The effects of such strategies, however, remain elusive, particularly when brief protocols are implemented due to the natural time constraints in school schedules. This study investigated the effects of a 3-minute mindful breathing protocol on learning and emotions implemented in a public primary school. Using a pre-post treatment-control design, 60 primary school students completed a battery of two self-reported emotion questionnaires (Positive and Negative Affect Schedule, PANAS-C, and State Mindfulness Scale, SMS), two iPad-based domain general cognitive tests (Flanker Inhibitory Control and Attention Test, FICAT, and Dimensional Change Card Sort Test, DCCST), and one self-reported domain specific cognitive test in mathematics. Continuous electrodermal activity (EDA), heart rate (HR), and heart rate variability (HRV) were also recorded throughout the protocol to measure autonomic arousal. Preliminary results show no significant changes in the PANAS-C, SMS, FICAT, and DCCST scores, and EDA and HR measures between the control and experimental groups pre-post protocol implementation. HRV measures of parasympathetic arousal significantly increased during mindful breathing consistent with expected shifts in respiratory sinus arrhythmia during slow-breathing tasks. The findings indicate that a 3-minute mindful breathing protocol fails to improve students’ learning and emotions. However, the protocol promotes physiological coherence consistent with other slow-breathing protocols in the literature. Future work should explore if longer protocols can have positive learning and emotional effects. Until then, schools should be careful dedicating resources to short or customized interventions without direct empirical support.