Humicola insolens feruloyl esterase was immobilized on chemically modified epoxy-activated supports of different pore sizes. Native and immobilized feruloyl esterases were investigated for their esterification activity on raffinose in surfactantless microemulsions. Pectic polysaccharides, obtained from cranberry pomace using chelating agent (CH) and diluted alkaline (DA) extractions, were then esterified at the optimized conditions. Using CH polysaccharide extract as a substrate, immobilized feruloyl esterase led to higher feruloylation (22.1–26.6%) than the free enzyme (4.2%), and yielded polysaccharides with a higher increase in the total phenolic content. Free and immobilized feruloyl esterases acted similarly in the feruloylation of polysaccharides present in the DA extract, identified as being rich in rhamnogalacturonan I neutral branches. The prebiotic activity score showed that cranberry pectic polysaccharides were better fermented than inulin and generated abundant propionic acid. Increased feruloylation of cranberry polysaccharides had a negative impact on the growth of Lactobacillus brevis and Bifidobacterium longum strains. The total short chain fatty acid concentration showed that the presence of feruloylation affected DA polysaccharides more than CH ones. This showed the importance of controlling the feruloylation extent as a compromise between the prebiotic and the antioxidant properties.