Freezing is the most commonly used method of preserving stone fruits. However, it is not the cheapest method. An alternative could be the pickling of fruits. Unfortunately, there is not much information in the literature on the effect of pickling on the health-promoting potential of stone fruits, including plums and cherries. This work focuses on assessing the impact of fruit pickling and storage on changes in the pro-health potential. Health-promoting properties were determined based on the content of anthocyanin dyes, vitamin C, total polyphenols, and the ability to inhibit free radicals. A substantial effect of pickling and storing pickled fruits on their health-promoting properties was observed. Pickling caused a decrease in the content of anthocyanins and vitamin C in the tested fruits. At the same time, the content of total polyphenols and the ability to reduce free radicals increased. It was also found that the content of bioactive compounds and the ability to reduce free radicals decreased during the storage of pickled cherries and plums. However, after 180 days of storage, pickled plums contained more polyphenols than fresh ones.