Meditation practices are often associated with changes in respiratory pattern, which are known to independently affect cardiovascular responses. In this study we aim to isolate the specific effect of meditation on the cardiovascular system by systematically controlling for the role of respiration. Forty participants without prior meditation experience were tested while pacing breathing at predetermined rates, in the presence or absence of Mantra meditation instructions, and in a body-scan meditation that did not involved controlled breathing. Continuous recordings were acquired for respiratory excursion, electrocardiogram, skin vasomotion, arterial and brain oxygenation and blood pressure. Mantra meditation decreased heart rate and cerebral tissue oxygenation compared to baseline, significantly more than paced breathing (p < 0.01). Moreover, meditation dampened the cardiorespiratory reactions to the concurrent control of breathing, preventing an increase in oxygen saturation and reducing the increase in chemoreflex sensitivity (p < 0.05), tidal volume (p < 0.01) and ventilation (p < 0.05), compared to paced breathing. Body-scan meditation reproduced the pattern observed during Mantra meditation, despite the absence of change in respiratory frequency compared to baseline. Post-meditation resting recordings showed a persistence of slowed heart rate (p < 0.001) and reduced respiratory rate (p < 0.001) compared to initial baseline. Meditation induces a hypometabolic state that does not solely depend on respiratory changes, but is linked to the meditation practice per se.