Abstract Feeding a liquid diet to the newborn calf has considerable implications for the development of the intestinal microbiota, as its composition can shift population to a highly adapted microbiota. Milk acidification may positively affect microorganisms that are beneficial to the intestine health. The present study evaluated 15 Holstein calves housed in tropical shelters, fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9 % CP; 18.5 % fat; diluted to 14% solids; n = 5) and III - whole milk acidified to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at the 8th week of age. After weaning, all calves were group housed and fed with starter concentrate and coast-cross hay ad libitum. To evaluate the microbioma, fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. The diversity indices and evenness were higher for whole milk when compared to milk replacer (P < 0,05), with no difference for acidified whole milk. Animal age affected all indices. Time 0 had higher richness and diversity (P < 0,001), while weeks 1 and 2 had the lowest (P < 0,001). Thirty-eight bacterial phyla were identified, and the most abundant in were Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria and Firmicutes C. It is possible to modify the microbiome by changing the liquid diet. However, differences according to calf age may show the best time for possible interventions in the diet to manipulate the intestinal microbiome to improve animal health and performance.