The green microalga Chromochloris zofingiensis is an emerging alternative to commercial astaxanthin due to its high productivity and metabolic flexibility with regard to growing in different nutritional modes, namely autotrophic, heterotrophic, and mixotrophic. Although the transition from one nutritional mode to another in each culture step (stock, preculture, and biomass production) can be easily realized and may trigger various metabolic functions, there have only been a few studies on its effects on growth and cell characteristics. Therefore, in this study, the effects of the transition of nutritional modes were investigated by transferring cells precultured in the three above-mentioned nutritional modes to the biomass production phase in the three modes. The heterotrophically precultured cells showed decreases in growth and biomass productivity when cultivated in prolonged dark cultures. Conversely, the heterotrophic cells showed a higher growth rate when irradiated in the autotrophic and mixotrophic biomass production phases, probably due to the accumulation of growth-promoting factors in the heterotrophic preculture. The mixotrophic biomass production phase showed higher maximum biomass productivity (1.28 g L−1 d−1) compared with the autotrophic (0.065 g L−1 d−1) and heterotrophic (0.448 g L−1 d−1) modes. The optimum conditions for stock, preculture and biomass production phase were autotrophic in order to maintain the following heterotrophic culture condition, heterotrophic to store growth-promoting factors, and mixotrophic to achieve high productivity, respectively.