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Growing butter markets, domestically and globally, provide opportunities for value-added variants of butter. Adding probiotics to butter could boosts its bioactivity; however, maintaining probiotic viability during storage is a major challenge. Mathematical analysis of probiotic population changes could help improve our understanding of how probiotics interact with butter and storage conditions. Two strains of probiotics in a 1:1 ratio as free cells or Whey Protein Hydrolysate–Maltodextrin (WPH-MD)-encapsulated cells, <i>Lactobacillus acidophilus</i> ATCC 4356 (LA5) and <i>Bifidobacterium animalis</i> ssp. <i>lactis</i> ATCC 27536 (BB12), were separately mixed into butter at 1% levels. Using analysis of covariance, a mathematical evaluation for probiotic population changes was performed by periodically determining viable counts, resulting in an adjusted R² value of 0.98 and demonstrating a strong relationship between the dependent variable (log₁₀ counts of probiotics) and independent variables (cell type, temperature of storage, and time of storage). After 21 days of storage, the number of free cells in butter dropped from 7.45 log₁₀ CFU/g to 0.56 log₁₀ CFU/g. On the other hand, it took 63 days for encapsulated cells to achieve 0.80 log₁₀ CFU/g at the same temperature. The same trend persisted at −18 °C, indicating that the WPH-MD encapsulant had a protective effect.