There is growing evidence that environmental changes caused by climate change can impact the microbiome of marine invertebrates. Such changes can have important implications for the overall health of the host. In the present study we investigated the impact of chronic exposure to an ambient (28°C) and a predicted mid- (30°C) and end-of-century (32°C) seawater temperature on microbiome modification in tissues of the cardiac stomach of the abundant predatory sea star Luidia clathrata collected in September 2018 from Apalachee Bay, Florida (29°58’N, 84°19’W) in the northern Gulf of Mexico (GOM). Diversity (Shannon index) was lowest among the microbial community of stomach tissue when compared to the microbiome of the artificial sea star feed, and aquarium sand and seawater across all three experimental temperature treatments. Moreover, the stomach microbial community composition was distinct between each of the four sample types. Exposure to the highest experimental temperature treatment (32°C) resulted in a significant modification of the composition of the microbial community in stomach and sand samples, but not in seawater samples when compared to those from the current mean ambient GOM temperature (28°C). Importantly, at the most elevated temperature the stomach microbiome shifted from a Vibrio sp. dominated community to a more diverse community with higher proportions of additional taxa including Delftia sp. and Pseudomonas sp. This microbiome shift could impact the digestive functionality and ultimately the health of L. clathrata, a key soft-bottom predator in the northern GOM.