In the present study, dark blue (BM) and white (WM) Myrtus communis (M. communis) pulps were added to probiotic goat milk ice cream formulations containing Lactobacillus casei (L. casei) 431 to evaluate prebiotic potentials of BM and WM fruits on L. casei 431. Additionally, the effects of storage and freezing process on viable L. casei 431 counts, total phenolic content (TPC) and antioxidant activity were examined. According to the results, it was determined that the BM and WM fruits had prebiotic potentials on L. casei 431. The freezing process of mixes reduced the counts of L. casei 431 by about 0.80–1.32 log CFU g−1 and this strain maintained high viability throughout the storage. After freezing process, TPC values of ice cream samples containing WM and BM fruits increased by 5.00 and 8.50 mg GAE 100 g−1, respectively. No alteration was detected in antioxidant activity during the storage.