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It has been shown that the interaction between marine phytoplankton and climate systems may intensify Arctic warming in the future via shortwave heating associated with increased spring chlorophyll bloom. However, the changes of chlorophyll variability and its impact on the Arctic future climate are uncomprehended. Lim et al. (Clim Dyn. 10.1007/s00382-018-4450-6, 2018a) (Part I) suggested that two nonlinear rectifications of chlorophyll variability play cooling role in present-day climate. In this study, we suggest that the decreased interannual chlorophyll variability may amplify Arctic surface warming (+ 10% in both regions) and sea ice melting (- 13% and - 10%) in Kara-Barents Seas and East Siberian-Chukchi Seas in boreal winter, respectively. Projections of earth system models show a future decrease in chlorophyll both mean concentration and interannual variability via sea ice melting and intensified surface-water stratification in summer. We found that suggested two nonlinear processes in Part I will be reduced by about 31% and 20% in the future, respectively, because the sea ice and chlorophyll variabilities, which control the amplitudes of nonlinear rectifications, are projected to decrease in the future climate. The Arctic warming is consequently enhanced by the weakening of the cooling effects of the nonlinear rectifications. Thus, this additional biological warming will contribute to future Arctic warming. This study suggests that effects of the mean chlorophyll and its variability should be considered to the sensitivity of Arctic warming via biogeophysical feedback processes in future projections using earth system models.