Peptidomics allows the identification of thousands of peptides that are derived from proteins. Urinary peptidomics has revolutionized the field of diagnostics as the sample represents complete systemic changes of the body and is collected non-invasively. We profiled the peptides in urine collected from different physiological states of Sahiwal cows namely heifer, pregnancy, and lactation. Endogenous peptides were extracted from 30 individual cows belonging to three groups, each group comprising of ten animals (biological replicates n = 10). Nano Liquid chromatography Mass spectrometry (nLC-MS/MS) experiments revealed 5239, 4774, and 5466 peptides in the heifer, pregnant, and lactating animals, respectively. The diversity in endogenous peptides in urine sets baseline information substantiating various bioactivities (anti-inflammatory, antimicrobial, antihypertensive, and anticancerous) associated with cow urine. Several proteases have been traced back in the body which was found responsible for the physiology specific peptide signature of urine. The in silico study also highlights the enrichment of progenitor proteins on the specific chromosome and their relative expression in context to specific physiology. The urinary peptides, precursor proteins, and proteases identified in the study thus set a solid foundation for future research in biomarker discovery and a better understanding of the pathophysiology of the body.