Abstract Background Lactation Consultants (LC) at Health Sciences Centre (HSC) and St Boniface General Hospitals (SBGH) supported the lactation of 2/3 of Manitoba newborns since 1994. The LC program in HSC was discontinued in 2018. Its impact on infant feeding in the province remains unclear. Methods To assess the influence of the LC program cessation on the feeding of newborns in postpartum wards via a retrospective administrative database cohort. Results A total of 126,285 infants were delivered in all Manitoban hospitals during 2014–2021 [First Nations (FN): 21%, all others: 79%, urban: 55%, rural: 41% and remote: 4%]. The rates of breastfeeding were lower and formula feeding were higher in FN and all other newborns after the program cessation (2018–2021) compared to that during 2014–2017 (p < 0.01). The intensity of the changes in infant feeding among FN or remote-living newborns during 2018–2021 were 2–threefold greater than that among all others or urban/rural-living newborns delivered in HSC (p < 0.01). In contrast, infant feeding status stayed stable for those delivered at SBGH where the LC program did not withdraw. The cessation of LC program decreased adjusted odds ratio (aOR) for exclusive breastfeeding in FN infants (aOR 0.93, 95% CI: 0.88–0.98) and urban-living infants (aOR 0.96, 95% CI: 0.94–0.98), but not in all others, rural- or remote-living infants. Increased odds for formula feeding was detected in FN and all other infants living in various regions in the province during 2018–2021 compared to that during 2014–2017 (p < 0.05). Conclusion The findings suggest that the discontinuation of LC program decreased breastfeeding and increased formula feeding, and the unfavorable changes in infant feeding was most profound among FN and remote-living infants.