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As global temperatures increase, sea ice loss will increasingly enable commercial shipping traffic to cross the Arctic Ocean, where the ships' gas and particulate emissions may have strong regional effects. Here we investigate impacts of shipping emissions on Arctic climate using a fully coupled Earth system model (CESM 1.2.2) and a suite of newly developed projections of 21st‐century trans‐Arctic shipping emissions. We find that trans‐Arctic shipping will reduce Arctic warming by nearly 1 °C by 2099, due to sulfate‐driven liquid water cloud formation. Cloud fraction and liquid water path exhibit significant positive trends, cooling the lower atmosphere and surface. Positive feedbacks from sea ice growth‐induced albedo increases and decreased downwelling longwave radiation due to reduced water vapor content amplify the cooling relative to the shipping‐free Arctic. Our findings thus point to the complexity in Arctic climate responses to increased shipping traffic, justifying further study and policy considerations as trade routes open. Plain Language Summary: Global warming is melting Arctic sea ice, thereby enabling greater maritime access to the Arctic Ocean. Emissions such as black carbon and sulfur from ships have the potential to warm the climate further by darkening snow and ice surfaces or cool the climate by promoting cloud formation. This study used a global Earth system model to simulate the climatic effects of emissions from ships crossing the Arctic Ocean from the present to 2099. We find that shipping emissions increase formation of clouds with high liquid water content, and cause the Arctic surface air to cool nearly 1° by 2099 relative to the shipping‐free Arctic. This cooling effect was amplified further by sea ice growth and reduced atmospheric water vapor. Our results illustrate the complexity of climatic responses to increased shipping in the Arctic and the need for greater understanding of the reciprocal nature of climate and human activities. Key Points: Climatic responses to projected trans‐Arctic shipping emissions are simulated using a fully coupled Earth system model (CESM 1.2.2)Shipping emissions reduce Arctic warming by nearly 1 °C by 2099 due to sulfate‐driven liquid water cloud formationSea ice growth‐induced albedo increases and reduced atmospheric water vapor amplify cooling relative to control runs [ABSTRACT FROM AUTHOR]