The effect of the fermented matrix on the color and the stability of anthocyanins contained in strawberry (Fragaria ananassa D.) and highbush blueberry (Vaccinium corymbosum L.) preparations for fruit yogurts, as well as soy-based (Glycine max L. Merr.) and bean-based (Phaseolus vulgaris L.) yogurt alternatives, stored for 8 weeks, was evaluated. To produce the fermented bean matrix, germinated seeds of white and black beans were used. The obtained fermented matrices had similar pH levels, while the soy-based and black bean-based yogurt alternatives were characterized by their high content of isoflavone aglycones and phenolic acids. The degradation of anthocyanins in strawberry and blueberry fermented products during storage followed first-order reaction kinetics. Significant differences were found depending on the fermented plant-based matrix. The fermented soy-based matrix demonstrated the highest T1/2 values for total anthocyanins (26.3 and 88.8 weeks for strawberry and blueberry products, respectively), whereas the yogurts exhibited the lowest values (13.3 and 49.3 weeks for strawberry and blueberry products, respectively). In the comparison of anthocyanin degradation during the storage of bean-based products, the pigments in the matrix obtained from fermented black beans showed better stability. During storage, the loss of anthocyanins was higher in strawberry products than in blueberry products, particularly with respect to malvidin and petunidin derivatives and acylated anthocyanins, which exhibited high stability. The total color difference (ΔE*) of blueberry plant-based products after an 8 week storage period ranged from 1.1 to 1.5. This data suggests that the addition of a coloring ingredient for industrial production may not be required.