To evaluate the utility of fruits and by-products/wastes as bioactive materials, we investigated the anti-allergic effects of hot-water and ethanol extracts from various fruit by-products and medicinal fruits using a β-hexosaminidase release assay. Bile acid-binding ability, which is related to the acceleration of bile acid excretion, was also determined for hot-water extracts. Among the extracts, the ethanol extract of grape bunch stem showed the highest (63.6%) inhibition of degranulation, as assessed by β-hexosaminidase release from rat basophilic leukemia cells (RBL-2H3) at a dose of 100 μg/mL. The hot-water extract from grape seed contained the highest total polyphenol content (353 mg gallic acid equivalent/g dry extract), but the total polyphenol content did not show a high correlation with the anti-degranulation effect. A positive relationship between the inhibitory effect of degranulation and proanthocyanidin content (0.1–0.3 in A550) was observed, but higher concentrations of proanthocyanidins in the system showed adverse effects. Proanthocyanidin content was also related to the bile acid-binding ability of the hot-water extracts with the highest value from Chinese quince hot-water extract (95%, 47.7 mg/g dry extract). These results suggest that proanthocyanidin-rich extracts from fruits and agro-industrial by-products have bioactive potential and can be exploited as anti-degranulation and bile acid-eliminating materials.