The addition of yogurt to fruit smoothies enhances their nutritional value by introducing components not naturally found in fruit products. However, the addition of fermented products can affect the stability of fruit bioactive components in fruits, such as anthocyanins. This study aimed to evaluate the effect of varying yogurt additions (0, 10, 20, and 30%) on the stability of anthocyanins during a 4-week refrigerated storage period. The smoothies were obtained from purees of strawberry, raspberry, and blueberry, combined with apple juice and apple puree. In addition, to elucidate the causes of the observed changes in the smoothies, model studies were conducted using purified anthocyanin extracts obtained from the analyzed fruits. We assessed the effects of pH, hydrogen peroxide concentration, and the addition of cell-free extracts from Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus on changes in anthocyanin content during storage. We found that adding yogurt led to a decrease in anthocyanin stability during the 4-week cold storage period. Specifically, a 30% yogurt addition decreased anthocyanin stability in all tested beverages, while a 20% yogurt addition impacted the strawberry and raspberry smoothies. The degree to which yogurt affected anthocyanin stability was dependent on the source of the raw material. The most notable impact was observed in strawberry smoothies and the least in blueberry smoothies. The variability could be attributed to differences in anthocyanin profiles among the fruits, the chemical composition of the beverages, and the observed difference in the survival rates of lactic acid bacteria. Model studies showed that during the storage of anthocyanin extracts, the addition of hydrogen peroxide and cell-free extract had a significant effect, whereas pH within the examined range (3.0-4.5) did not affect anthocyanin stability.