<jats:title>Abstract</jats:title><jats:p>Marine heatwaves (MHWs), defined as extreme ocean warming episodes, have strengthened over the past decades. High-resolution climate models improve understanding of MHWs under global warming, but such events in the future Arctic are currently overlooked. In a high-resolution climate model, we find Arctic MHWs intensify on orders of magnitude during the warming twenty-first century, following sea ice retreat. However, with little sea ice coverage, strong interannual variability emerges, which could surpass the amplitude of former intensification. Furthermore, the enhancement of MHWs correlates with an order of magnitude increase in the rate of change in the temperature anomaly. Additionally, MHWs are found to be accompanied by stratification enhancement, which could surpass interannual variability of future stratification. Such extreme temperature fluctuations combined with stratification enhancement suggest major challenges for Arctic ecosystems, and may negatively impact food webs through direct physiological temperature effects, as well as indirectly through nutrient supply and taxonomic shifts.</jats:p>