Bovine milk fat globule membrane (MFGM) proteins are crucial to calf health and human nutrition, but a knowledge gap exists for its lactation stage-specific variations in cows and buffaloes. This study employed mass spectrometry to identify the inter- and intra-lactation stage-specific MFGM proteins in Murrah buffalo (Mu) and Holstein Friesian cow (HF). Mu exhibited higher proteins (n=264) than HF (n=250); utilizing multivariate analysis, differentially abundant proteins (n=78 in HF, n=31 in Mu) were identified specific to lactation stages. The MFGM proteins were categorized into health-associated (47.1%), lipid-associated proteins (44.1%), and shared proteins (8.8%). HF milk contained all health-associated proteins detected in Mu, besides possessing unique proteins (e.g., BTN1A1, SAA3, and ENPP3), including lipid-associated proteins that contributed to improved calf immunity. These results suggest HF milk is more suitable for calf health and dairy product development, including expanding our understanding of lactation stage-specific MFGM proteins and highlighting their potential health benefits.