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Yarrowia lipolyticaexcels in microbial lipid production, thriving across diverse conditions. Batch or fed-batch fermentation is the not only common practice to achieve higher lipid titer and yield but it is also subject to lower lipid productivity. Single-stage continuous fermentation (CF) provides a great potential for significantly higher productivity, but genetic instability is often seen and challenges strain performance over the long-period CF. This study harnesses single-stage CF to not only improve lipid productivity but also evolve high-lipid mutants from a previously engineeredY. lipolyticastrain E26 via adaptive laboratory evolution (ALE) in a continuous bioreactor, guided by a predictive kinetic model. The single-stage CF was run for 1128 hours (47 days) with key process parameters adjusted in a 1-L bioreactor to produce over 150 g/L yeast biomass, exceeding the targeted 113 g/L that is predicted by the model. Compared with the fed-batch fermentation process, the single-stage CF successfully improved lipid productivity from 0.3–0.5 g/L/h to about 1 g/L/h while maintaining the lipid yield at around 0.1 g/g. The CF sample at 1008 hours was used to isolate mutants with higher lipid production after ALE in the continuous bioreactor. A mutant E26E03 was identified, which demonstrated improvements in biomass, lipid content, and lipid yield by 43%, 30%, and 51%, respectively, over the original strain E26 in fed-batch fermentation. Our study indicated that using model-guided CF with ALE in a continuous bioreactor provides a great potential for significantly higher product titer, rate, and yield in biomanufacturing.