The objective of the current study was to investigate the impact of dietary methionine supply during late-pregnancy in dairy cows on gut microbiome and metabolome composition and their association with growth performance in neonatal calves from birth to weaning. Twenty-six Holstein heifer calves (n = 13/treatment) born to cows receiving a control diet (CON) or CON plus ethylcellulose rumen-protected methionine (MET; Mepron®, Evonik Industries AG, Germany) during the last 4-weeks of pregnancy. Calves received 3.8 L of first-milking colostrum from the respective dam within 8 h after birth. Calves were housed in individual outdoor hutches bedded with straw, fed twice daily with a milk replacer and had ad libitum access to a starter grain mix throughout the study. Fecal samples were collected at d 0 (i.e., at birth before colostrum feeding), 14, 28, and 42 (before weaning). Genomic DNA from fecal samples was used for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene using Illumina MiSeq. Sequencing data were processed and analyzed with QIIME 2 software using the DADA2 pipeline. Calves from MET-fed cows had greater dry matter intake and average daily gain from birth to weaning. Chao1 and OTU index analyses indicated that MET compared with CON heifers had a more diverse microbiota. Compared with CON, MET heifers had greater relative abundance of Fusobacterium, Ruminococcus, and Akkermansia, and lower abundance of Fecalibacterium, Blautia, Arthrobacter, and Clostridium. No differences were detected between groups in the abundance of Dorea, Bifidobacterium, Oscillospira, Succinivibrio, Butyricicoccus, and Brachybacterium. Overall, results indicate that maternal supply of methionine altered the diversity and structure of gut microbiota in neonatal heifers. The mechanistic link between maternal methionine supply, performance, and gut metabolome remains to be determined.