Coconut skim milk (CSM), a high-moisture by-product of wet centrifugation-based virgin coconut oil processing, requires appropriate post-pasteurization storage to maintain its quality and microbiological safety for further food utilization. This study evaluated the stability of pasteurized CSM under refrigerated storage at 4 °C over 28 days, focusing on physicochemical, color, and microbiological changes. Pasteurized CSM treatments (e.g C1T1=70°C at 5mins; C1T2=70°C at 10mins; C2T1= 80°C at 5mins; C2T2 = 80°C at 10mins) were monitored for pH, titratable acidity, L* value, hue angle, chroma, aerobic plate count, total coliforms, and yeast and molds. Results showed that pH remained relatively stable during refrigerated storage, with no significant Day 0–Day 28 changes in most treatments, except C2T2, which showed a significant decrease (p < 0.05). In contrast, titratable acidity significantly increased in C1T1, C1T2, and C2T1 (p < 0.05), indicating progressive acid development despite limited pH variation. Color changes were also observed, particularly in chroma, which significantly changed in C1T1, C2T1, and C2T2 (p < 0.05). Microbiological results further showed significant logarithmic increases in aerobic plate count, total coliforms, and yeast and molds during storage. Refrigerated pasteurized CSM remained relatively safe up to Day 7, after which microbial increases indicated progressive deterioration. Overall, refrigeration slowed but did not prevent quality loss, supporting only short-term refrigerated storage or the need for further preservation.