The aim of this work was to study the colonisation of the rumen by the three main microbial groups over the first 4 weeks of life and to assess to what extent the type of feeding management (natural with the mother, NAT, or artificial with milk replacer, ART) exerts an effect. Thirty pregnant goats carrying two fetuses were selected. At birth, one kid was taken immediately away from the doe and fed milk replacer (ART), while the other kid remained with the mother (NAT). Groups of four kids (from ART and NAT experimental groups) were slaughtered at 1, 3, 5, 7, 14, 21 and 28 days of life, resulting in seven sampling times. On the sampling day, after slaughtering, the rumen was weighed full and empty and the content sampled and pH measured. Aliquots of rumen digesta were immediately frozen for DNA and volatile fatty acid (VFA) analyses. The weight of the rumen was higher in NAT kids from Day 21 onward, while no difference was observed for rumen content volume. The three microbial groups (bacteria, archaea and protozoa) were detected from Day 1 in both experimental groups. The concentration of bacteria was higher in the rumen of NAT kids on Days 3, 5, 7 and 14 and of protozoa from Day 3 onward. This was reflected in greater VFA concentrations and lower pH in the rumen of NAT kids from Day 3. Our results confirmed substantial microbial colonisation from the first day of life in the undeveloped rumen. The feeding management (natural vs artificial) before weaning had an effect on microbial colonisation and rumen fermentation and, therefore, it should be considered when designing nutritional intervention strategies in early life.