Membrane lipid remodeling contributes to the environmental acclimation of plants. In the green lineage, a betaine lipid, diacylglyceryl-N,N,N-trimethylhomoserine (DGTS), is included exclusively among green algae and nonflowering plants. Here, we show that the green alga Chlorella kessleri synthesizes DGTS under phosphorus-deficient conditions through the eukaryotic pathway via the ER. Simultaneously, phosphatidylcholine and phosphatidylethanolamine, which are similar to DGTS in their zwitterionic properties, are almost completely degraded to release 18.1% cellular phosphorus, and to provide diacylglycerol moieties for a part of DGTS synthesis. This lipid remodeling system that substitutes DGTS for extrachloroplast phospholipids to lower the P-quota operates through the expression induction of the BTA1 gene. Investigation of this lipid remodeling system is necessary in a wide range of lower green plants for a comprehensive understanding of their phosphorus deficiency acclimation strategies., Oishi et al. report that the synthesis of a betaine lipid, diacylglyceryl-N,N,N-trimethylhomoserine (DGTS) in a green alga Chlorella kessleri replaces phosphatidylcholine and phosphatidylethanolamine, the two most abundant phospholipids, during phosphate deprivation. This study provides insights into the understanding of the phosphorus-deficiency acclimation strategies via lipid remodeling in lower green plants.