Key points Arterial PCO2 is kept constant via breathing adjustments elicited, at least partly, by central chemoreceptors (CCRs) and the carotid bodies (CBs). The CBs may be active in a normal oxygen environment because their removal reduces breathing. Thereafter, breathing slowly returns to normal. In the present study, we investigated whether an increase in the activity of CCRs accounts for this return. One week after CB excision, the hypoxic ventilatory reflex was greatly reduced as expected, whereas ventilation and blood gases at rest under normoxia were normal. Optogenetic inhibition of Phox2b‐expressing neurons including the retrotrapezoid nucleus, a cluster of CCRs, reduced breathing proportionally to arterial pH. The hypopnoea was greater after CB excision but only in a normal or hypoxic environment. The difference could be simply explained by the loss of fast feedback from the CBs. We conclude that, in rats, CB denervation may not produce CCR plasticity. We also question whether the transient hypoventilation elicited by CB denervation means that these afferents are active under normoxia. Abstract Carotid body denervation (CBD) causes hypoventilation and increases the arterial PCO2 set‐point; these effects eventually subside. The hypoventilation is attributed to reduced CB afferent activity and the PCO2 set‐point recovery to CNS plasticity. In the present study, we investigated whether the retrotrapezoid nucleus (RTN), a group of non‐catecholaminergic Phox2b‐expressing central respiratory chemoreceptors (CCRs), is the site of such plasticity. We evaluated the contribution of the RTN to breathing frequency (FR), tidal volume (VT) and minute volume (VE) by inhibiting this nucleus optogenetically for 10 s (archaerhodopsinT3.0) in unanaesthetized rats breathing various levels of O2 and/or CO2. The measurements were made in seven rats before and 6–7 days after CBD and were repeated in seven sham‐operated rats. Seven days post‐CBD, blood gases and ventilation in 21% O2 were normal, whereas the hypoxic ventilatory reflex was still depressed (95.3%) and hypoxia no longer evoked sighs. Sham surgery had no effect. In normoxia or hypoxia, RTN inhibition produced a more sustained hypopnoea post‐CBD than before; in hyperoxia, the responses were identical. Post‐CBD, RTN inhibition reduced FR and VE in proportion to arterial pH or PCO2 (ΔVE: 3.3 ± 1.5% resting VE/0.01 pHa). In these rats, 20.7 ± 8.9% of RTN neurons expressed archaerhodopsinT3.0. Hypercapnia (3–6% FiCO2) increased FR and VT in CBD rats (n = 4). In conclusion, RTN regulates FR and VE in a pH‐dependent manner after CBD, consistent with its postulated CCR function. RTN inhibition produces a more sustained hypopnoea after CBD than before, although this change may simply result from the loss of the fast feedback action of the CBs.