Temperate fisheries grounds are exposed to compound effects of jellyfish proliferations and fishing pressure, which affect local fisheries, cause economic losses, and threaten seafood supply. Here, we quantify the interlink between climate variability and jellyfish blooms and their impact on the Japanese anchovy (Engraulis japonicus), in the Korean coastal waters. We used a bioclimate dataset (2010–2019) that includes quantitative information of two major bloom-former species, Aurelia coerulea and Nemopilema nomurai, in the Korean Peninsula. We show that climate phenomena governing East Asia regions explain circa half of jellyfish variability. In turn, jellyfish blooms have a significant negative effect on anchovy interannual changes (r = -0.47, P < 0.01), which varies along with the bloom magnitude. Our results indicate that the intensity of jellyfish blooms, more than their duration, has a predominant effect on anchovy and coastal fisheries production. We also suggest the possibility of using climate signals for assessing and eventually predicting, interannual abundance changes of jellyfish in the Korean Peninsula. These results stress the challenge posed by jellyfish blooms to the provisioning of ecosystem services via their influence on marine harvested fish and further highlight the need for their integration into ecosystem-based management.