Climate-driven range extensions of animals into higher latitudes are often facilitated by phenotypic plasticity. Modifications to habitat preference, behaviour and diet can increase the persistence of range-extending species in novel high-latitude ecosystems. These strategies may be influenced by changes in their gut and stomach microbial communities that are critical to host fitness and potentially adaptive plasticity. Yet, it remains unknown if the gut and stomach microbiome of range-extending species is plastic in their novel ranges to help facilitate these modifications. Here, we categorised stomach microbiome communities of a prevalent range-extending coral reef fish along a 2000-km latitudinal gradient in a global warming hotspot, extending from their tropical core range to their temperate cold range edge. At their cold range edge, the coral reef fish's stomach microbiome showed a 59% decrease in bacterial diversity and a 164% increase in the relative abundance of opportunistic bacteria (Vibrio) compared to their core range. Microbiome diversity was unaffected by fish body size, water temperature, physiology (cellular defence and damage) and habitat type (turf, barren, oyster, kelp and coral) across their range. The observed shifts in microbiome composition suggest dysbiosis and low plasticity of tropical range-extending fishes to novel environmental conditions (e.g., temperate prey and lower seawater temperature) at their novel range edges, which may increase their susceptibility to disease in temperate ecosystems. We conclude that fishes extending their ranges to higher latitudes under ocean warming can experience a simplification (i.e., reduced diversity) of their stomach microbiome, which could restrict their current rate of range extensions or establishment in temperate ecosystems.