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Abstract Background Current efforts on the optimization of the two-stage cultivation using stress-induced lipid accumulation have mostly focused only on the lipid induction stage. Although recent studies have shown that stress-induced lipid accumulation is affected by the physiological status of the cells harvested at the preceding cultivation stage, this issue has hardly been examined hitherto. Such a study needs to be carried out in a systematic way in order to induce lipid accumulation in a consistent and predictable manner with regard for variances seen at the cultivation stage. Results After a photoautotrophic cultivation of Chlorella sorokiniana HS1 in a modified BG11, harvested cells were re-suspended in the fresh medium, and then NaCl was added as the sole stress inducer with light illumination to induce additional accumulation of lipid. Effects of culture temperature on the lipid accumulation were analyzed by the Kruskal–Wallis test. From the microscopic observation, we had observed a definite increase in lipid body induced by the stress since the cell entered a stationary phase. A multiple linear regression model was developed so as to identify significant parameters to be included for the estimation of lipid induction. As a result, several key parameters at the end of cultivation, such as cell weight, total lipid content, chlorophyll a in a cell, and Fv/Fm, were identified as the important proxy variables for the cell’s physiological status, and the modeling accuracy was achieved by 87.6%. In particular, the variables related to Fv/Fm were shown to have the largest influence, accounting for 65.7% of the total variance, and the Fv/Fm had an optimal point of maximum induction at below its average. Clustering analysis using the K-means algorithm indicated that the algae which are 0.15 pg cell−1 or less in chlorophyll concentration, regardless of other conditions, had achieved high induction results. Conclusion Experimental results showed that it usually achieves high lipid induction after the cells naturally end their division and begin to synthesize lipid. The amount of lipid induction could be estimated by the selected proxy variables, and the estimation method can be adapted according to practical situations such as those with limited measurements.