We used a microplate-based method to quantify microalgal lipids with Nile Red staining and a fluorescence microplate reader. However, a method to quantify starch that combines microplates with staining has not been reported. Therefore, we examined microplate-based quantification of lipids using Nile Red staining and of starch using Lugol staining. Neither starch nor lipids accumulated during the zero phase of cultured Parachlorella kessleri, only starch accumulated during the starch phase, and starch was subsequently lost and lipids accumulated during the oil phase. The quantities of starch and lipids were measured using a microplate-based method, which indicated linear production of starch and lipids within limited ranges (lipids, 0.071–0.380 g mL⁻¹; starch, 155–404 mg mL^－1) when standard curves were prepared for lipids extracted with methyl tertiary-butyl ether and for starch extracted with anthrone. The concentration of starch produced during the starch phase was 0.59 mg mL⁻¹ and that of lipids during the oil phase was 2.49 mg mL⁻¹. The concentration of starch produced was 0.05–0.13 mg mL⁻¹ during phases other than the starch phase, and lipids were not detected other than during the oil phase because lipid contents were approximated based on the quantity of triacylglycerol, which stains with Nile Red.