Plasticity is a fundamental property of the neural system controlling breathing. One key example of respiratory motor plasticity is phrenic long-term facilitation (pLTF), a prolonged increase in phrenic nerve activity following intermittent exposure to low oxygen (acute intermittent hypoxia, AIH). pLTF arises from distinct intracellular signaling cascades initiated by serotonin and adenosine, respectively, that interact via powerful crosstalk inhibition. We demonstrate serotonin versus adenosine balance varies dramatically with time-of-day and the specific AIH protocol. The fundamental mechanism driving pLTF shifts from serotonin-dominant, adenosine-constrained during rest, to adenosine-dominant, serotonin-constrained in the active phase using our standard AIH protocol. This mechanistic flip results from both daily changes in basal spinal adenosine levels across time-of-day and hypoxia-evoked adenosine release. Since AIH is emerging as a promising therapeutic modality to restore respiratory and non-respiratory movements in people with spinal injury and ALS, new knowledge that time-of-day and protocol impact pLTF mechanisms has experimental, biological and translational implications.