Symbiotic mutualistic associations prevail in nature, but how organisms overcome stress while maintaining symbiotic relationships is poorly understood. The marine acoel C. longifissura hosts a large population of obligate extracellular endosymbiotic green algae. This acoel is able to regenerate all missing body parts from small tissue fragments, while the algae repopulate the newly formed tissue. To understand how these two organisms coordinate their responses to injury and cooperate during tissue regeneration, we used nanopore long-read RNA sequencing to measure transcriptomic changes in both organisms during early stages of acoel regeneration. While the acoel wound response appeared to be highly conserved and driven by a homolog of early growth response transcription factor, the algae upregulated metabolic pathways associated with photosynthesis. Chemically blocking photosynthesis did not change the rate of acoel regeneration, but quickly reduced the algal density. In contrast, under homeostatic conditions, photosynthesis inhibition did not cause a similar reduction in the algal population. Since acoels are capable of ingesting algae, our results suggest that consumption of the symbiotic algae may be a strategy to satisfy the higher metabolic demands during acoel regeneration. A compensatory increase in photosynthesis, and thereby algal proliferation, are required to support acoel regeneration and maintain the symbiotic relationship during this stress condition.