Bioeroding sponges directly interact and compete with corals on tropical reefs. Experimental studies have shown climate change alters this biotic interaction, often in favor of the sponge. Ocean acidification (OA) in particular increases sponge bioerosion and reduces coral calcification, yet little is known about the molecular basis of these physical changes. Here, we use RNA-seq data to understand how OA impacts the interaction between the bioeroding sponge, Cliona varians, and branching coral, Porites furcata, at the transcriptomic level. Replicate sponge and coral genets were exposed to ambient (8.1 pH) and acidified (7.6 pH) conditions in isolation and in treatments where they were physically joined for 48h. We found the coral had a low transcriptomic response (tens of transcripts) to the sponge, suggesting the coral does little to actively deter sponge overgrowth. By contrast, the sponge differentially expressed 7320 transcripts in response to the coral under ambient conditions and 3707 transcripts in response to acidification. Overlap in the responses to acidification and coral stimuli, 2500 transcripts expressed under both treatments, suggests a similar physiological response to both cues. The sponge expressed 50x fewer transcripts in response to the coral under acidification, indicating energetic costs of bioerosion for sponges are lower under OA. Our results demonstrate how acidification drives ecosystem-level changes in the accretion/bioerosion balance on coral reefs. This shift is not only the result of changes to the thermodynamic balance of these chemical reactions but also the result of active physiological responses of organisms to each other and their abiotic environment.