Chokeberries are an excellent source of polyphenols, but their fate during juice processing and storage is unknown. The stability of anthocyanins, total proanthocyanidins, hydroxycinnamic acids, and flavonols at various stages of juice processing and over 6 months of storage at 25 °C was determined. Flavonols, total proanthocyanidins, and hydroxycinnamic acids were retained in the juice to a greater extent than anthocyanins, with losses mostly due to removal of seeds and skins following pressing. Anthocyanins were extensively degraded by thermal treatments during which time levels of protocatechuic acid and phloroglucinaldehyde increased, and additional losses occurred following pressing. Flavonols, total proanthocyanidins, and hydroxycinnamic acids were well retained in juices stored for 6 months at 25 °C, whereas anthocyanins declined linearly. Anthocyanin losses during storage were paralleled by increased polymeric color values, indicating that the small amounts of anthocyanins remaining were present in large part in polymeric forms.