Anthropogenic habitat loss and resource decline as well as ecological imbalances such as overpopulation threaten many mammal populations. One practical strategy available to environmental managers to promptly alleviate these threats is to translocate animals. However, in some instances the translocated animals fail to thrive. Such translocation failures may be caused by unappreciated differences between the source and destination areas. For instance, if the diet available to the animals at the destination location is different from that at the source then translocated animals may not be able to cope with the change. This is likely to be true for specialist herbivores that rely on their gastrointestinal microbiome to digest and detoxify otherwise unpalatable material, particularly if the animals’ microbiomes are unsuited to the new diet and cannot rapidly adapt. The koala is one such herbivore that has often been translocated throughout southern Australia due to their over-browsing of particular eucalypt species, leading to habitat destruction and starvation. Previous work in our laboratory has shown that koalas feeding on different species of eucalypt have functionally and compositionally different microbiomes. In the current study we tracked how the microbiomes of 17 koalas changed over the course of a year after translocation relative to 12 control animals. We investigated whether the initial community composition of the animals’ microbiomes influenced the diet, condition or survival of the koalas following translocation. This study will improve our understanding of how the gastrointestinal microbiome impacts a mammal’s ability to shift diets after translocation or natural migration.