The symbiosis between anemonefishes and giant sea anemones provides an excellent opportunity for studying acclimation and plasticity. After a two-week oceanic larval phase, anemonefish recruits return to the reef to settle into a host. This host choice has profound impact on the fish. Many anemonefish species, including the widely distributed generalist Amphiprion clarkii, have two different colour morphs depending on the host species. Recently, we demonstrated that this pigmentation is plastic and can change when the fish are moved into a different host species. However, the effects of the host anemone go way beyond just the pigmentation. Here we present the results from our transcriptomic analyses of A. clarkii. We placed naïve juveniles without previous anemone contact in different host anemone species for three weeks, to characterise whole body and organ-specific gene expression. Within this short period, we observed significant expression changes in genes related to metabolism when looking at both, whole body and liver. Furthermore, genes involved in immune responses are also differentially expressed, providing a potential mechanistic link to the colour change. Together, this shows that the seemingly random settlement of new anemonefish recruits into host anemones has significant physiological consequences. We expect that many fish species experience similar environmentally driven transcriptomic effects. However, the common movement between microhabitats in most fishes, makes such environment-specific influences much harder to disentangle than in anemone-associated anemonefish.