While microbiome associations are known to impact species survival, the extent to which microbiome variation aids in invasion dynamics is largely unknown. Here, we studied the microbiome diversity and composition of native and invasive raccoon populations to assess the microbiome's role in invasion success. We found that native and invasive populations possess highly distinct microbiomes, with the invasive populations displaying greater gut and oral microbiota diversity without signs of instability or functional decline. Significant differences were found between the microbiota of each pair of invasive populations. The core microbiome of introduced populations consisted of a higher number of taxa than that found in native populations, suggesting a lack of microbiome deterioration in invasive populations. However, this may also reflect insufficient time for the establishment of a stable microbiome. Nevertheless, we found no evidence of reduced diversity of the microbiota linked to the population bottleneck or of increased microbiome dispersion indicating lower community stability. Native populations exhibited no microbiome differentiation between distant locations and showed lower, but still reasonably high, alpha diversity, suggesting the stability of the microbiome. Our findings imply that the invasion process changed the microbiota composition while preserving functional capability across different populations. This study highlights the microbiome as a potential factor aiding the adaptation of invasive populations.