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The dairy industry relies on the health and well-being of dairy cows for the optimal production of milk and dairy products. Mastitis, a prevalent and economically burdensome disease characterized by udder inflammation, poses significant challenges to dairy farmers worldwide. In this study, we employed peptidomics to explore the peptide profiles of dry secretions collected from dairy cows at specific intervals during the dry-off period. We hypothesized that alterations in peptide composition during the dry period may influence pathogen proliferation and immune cell functioning, thereby impacting mastitis susceptibility. Our objectives were to investigate the following: (i) differences in peptide composition and alterations between healthy cows and those with subclinical mastitis, potentially serving as biomarkers for early mastitis detection and offering insights into udder bioprocesses; (ii) variations in peptide profiles between the early (day 2) and later (day 21) stages of the dry-off period during both health conditions. Dry secretions were collected from 16 udder quarters of 8 cows at two defined time points—Day 2 (D2) and Day 21 (D21)—during the dry period. Our results revealed distinct peptide patterns between healthy and subclinical mastitis cows, as well as temporal variations in peptide profiles throughout the dry-off period. A total of 1235 peptides, originating from 59 distinct proteins (primarily β-casein), were detected across the four groups: subclinical mastitis day 21 (SCM-D21), subclinical mastitis day 2 (SCM-D2), healthy day 21 (H-D21), and healthy day 2 (H-D2). Furthermore, 56 out of the 1235 peptides identified in total matched known functional peptides, with a total of 17 different functions including antimicrobial, antioxidant, and immunomodulatory, suggesting their potential roles in mastitis pathogenesis and mammary gland physiology. Comparative analyses revealed changes in the levels of these functional peptides across the four different groups, suggesting their potential roles in regulating immune responses, oxidative stress, inflammatory processes, and other biological activities during subclinical mastitis and the dry-off period. These findings provide valuable insights into mastitis detection, management strategies, and dairy cow health monitoring, offering promising avenues for enhancing milk quality and dairy industry sustainability.