Polyphenols from Saskatoon berry are promising functional ingredients, yet their value depends on stability during processing, digestion, and transepithelial transfer. This study evaluated freeze-dried inulin (INU) and inulin/galactooligosaccharide (INU/GOS) matrices as carriers for purified Saskatoon berry phenolics. Powders containing 5–25% GOS were characterized by SEM, simulated gastrointestinal digestion, Caco-2 transport, antioxidant and anti-inflammatory assays, prebiotic testing, and cytocompatibility assessment. Initial phenolic retention remained high (88.5–92.7%). Digestion markedly reshaped the profile: apparent total polyphenol bioaccessibility reached 106.2–122.6%, anthocyanins were the least stable fraction, and phenolic acids together with selected flavonols dominated the post-digestive pool. Transepithelial transfer was selective; INU90:GOS10 showed the most favorable overall transfer profile, whereas INU80:GOS20 yielded the highest absolute phenolic content after transport. GOS-containing systems improved selected antioxidant, anti-inflammatory, and prebiotic responses, while pure inulin showed the highest cytocompatibility. Overall, carrier composition modulated the post-digestive functionality of Saskatoon berry polyphenols.