The increasing concentrations of greenhouse gasses such as nitrous oxide (N2O) is changing our climate. While the impacts of climate change are much more apparent at a macro level, climate change is also impacting the way microorganisms function, for example, by altering their abundances and diversity due to warming. In this study, we characterised the microbiome of a marine ascidian, Herdmania grandis, which is increasing in abundance in Australian temperate waters impacted by warming and which hosts a microbial community that produces high concentrations of N2O. We used 16S rRNA gene amplicon sequencing to explore H. grandis’ microbiome. In addition to analysing field samples, we performed a manipulative experiment to assess the impact of warming on N2O production and the microbiome across different body sections. We found that H. grandis has a diverse microbiome consisting of both novel taxa and those known to be important in nitrogen cycling (e.g. Nitrosospira sp.), with different body sections hosting distinct microbial communities, however, there was no difference in the microbial communities at different temperatures. Therefore, this study aids in better understanding the role of marine invertebrate microbiomes and their associated N2O production.