Buttermilk is a potential material for the production of a milk fat globule membrane (MFGM) and can be mainly classified into two types: whole cream buttermilk and cheese whey cream buttermilk (WCB). Due to the high casein micelle content of whole cream buttermilk, the removal of casein micelles to improve the purity of MFGM materials is always required. This study investigated the effects of rennet and acid coagulation on the lipid profile of buttermilk rennet-coagulated whey (BRW) and buttermilk acid-coagulated whey (BAW) and compared them with WCB. BRW has significantly higher phospholipids (PLs) and ganglioside contents than BAW and WCB. The abundance of arachidonic acid (ARA)-and eicosapentaenoic acid (EPA)-structured PLs was higher in WCB, while docosahexaenoic acid (DHA)-structured PLs were higher in BRW, indicating that BRW and WCB intake might have a greater effect on improving cardiovascular conditions and neurodevelopment. WCB and BRW had a higher abundance of plasmanyl PL and plasmalogen PL, respectively. Phosphatidylcholine (PC) (28:1), LPE (20:5), and PC (26:0) are characteristic lipids among BRW, BAW, and WCB, and they can be used to distinguish MFGM-enriched whey from different sources.