Ocean higher temperature and acidity levels affect its carbonate chemistry, and calcifying organisms that depend on the calcium carbonate saturation state (ΩCaCO3) to build their skeleton may be vulnerable to these changes. Despite their important roles in the marine environment, little is known about the vulnerability of calcareous sponges under these stressors. We performed an acute short-term experiment (9 days) with thermal and pH stresses to explore their effects on the skeleton and microbiome of the calcareous sponge Sycettusa hastifera. We observed that sponge spicules showed no corrosion and no Mg/Ca ratio variation when exposed to stress conditions. However, the outermost spicules were smaller in low pH treatment, although these effects were often diminished when higher temperatures were also applied. In general, the sponges synthesized normally shaped spicules under stress conditions, but the proportion of deformed spicules increased significantly in elevated temperature. In addition, we observed a stable host–microbiome association in which there is microbiome flexibility under thermal and pH stresses with a significantly increase in abundance of some associated bacteria. Our results suggest that S. hastifera has low vulnerability under the future ocean conditions here designed, since it showed indications of resistance that could help them adapt and survive.