During a food product's life, storage conditions affect its composition of nutrients, bioactive compounds, and sensory attributes. In this research, strawberry and apple purees were selected as a model to examine how the storage of various purees industrially produced with different technologies affect the bioactive phenolic compounds, color, and sensory attributes. Specifically, fruit products processed on an industrial scale by different technologies including freezing, thermal treatment (mild and standard), and high-pressure processing were studied, as well as storage for up to 12 months at -20, 4, and 24 °C. In strawberry puree, storage conditions had a stronger impact on phenolic compound levels, particularly on anthocyanins, whereas in apple puree, the initial processing techniques exerted a greater influence than storage conditions, mainly caused by the hot or cold crushing processes. In general, proanthocyanidins were the major phenolic group and the most stable during storage, while anthocyanins were the group most affected by both processing and storage. Apple flavonols and dihydrochalcones were quite stable, while strawberry ellagitannins suffered higher degradations during storage. Through our analysis, it is found that during storage, the stability of polyphenols in each fruit is different, and processing and storage can be either detrimental or even beneficial. The selection of the ideal storage conditions (time and temperature) is a key factor to maintaining the polyphenol content in sensitive fruits such as strawberries. However, storage conditions are in some cases more important to minimizing the polyphenol losses than how the product is processed.