Ongoing and future changes in wind and temperature are predicted to alter upper ocean vertical mixing across the Southern Ocean. How these changes will affect primary production (PP) remains unclear as mixing influences the two controlling factors: light and iron. We used a large ensemble of 1‐D‐biogeochemical model simulations to explore the impacts of changes in mixed‐layer depths on PP in the Southern Ocean. In summer, shoaling mixed‐layer depth always reduced depth‐integrated PP, despite increasing production rates. In winter, shoaling mixed layers had a two‐staged impact: for moderate shoaling PP increased as light conditions improved, but more pronounced shoaling decreased iron supply, which reduced PP. The fraction of PP exported below 100 m also presented a nonmonotonic behavior. This suggests a potential future shift from a situation where reduced winter mixing increases PP and export, to a situation where PP and export may collapse if the ML shoals above a threshold depth.