The master circadian clock, located in the suprachiasmatic nuclei (SCN), organizes the daily rhythm in minute ventilation (VE). However, the extent that the daily rhythm in VE is secondary to SCN-imposed O2 and CO2 cycles ( i.e., metabolic rate), or driven by other clock mechanisms, remains unknown. Here, we experimentally shifted metabolic rate using time-restricted feeding (without affecting light-induced synchronization of the SCN) to determine the influence of metabolic rate in orchestrating the daily VE rhythm. Mice eating predominantly at night exhibited robust daily rhythms in O2 consumption (VO2), CO2 production (VCO2), and VE with similar peak times (~ZT18) that were consistent with SCN organization. However, feeding mice exclusively during the day separated the relative timing of metabolic and ventilatory rhythms, resulting in a ~8.5-hr advance in VCO2, and a disruption of the VE rhythm, suggesting opposing circadian and metabolic influences on VE. To determine if the molecular clock of cells involved in the neural control of breathing contribute to the daily VE rhythm, we examined VE in mice lacking BMAL1 in Phox2b-expressing respiratory cells ( i.e., BKOP mice). The ventilatory and metabolic rhythms of predominantly night-fed BKOP mice did not differ from wild-type mice. However, in contrast to wild-type mice, exclusive day feeding of BKOP mice led to an unfettered daily VE rhythm with a peak time aligning closely with the daily VCO2 rhythm. Taken together, these results indicate that both daily VCO2 changes and intrinsic circadian time-keeping within Phox2b respiratory cells are predominant orchestrators of the daily rhythm in ventilation.