D-Raffinose is widely used in the food and pharmaceutical industries due to its functional properties. It serves as a prebiotic, promoting the growth of beneficial gut bacteria such as bifidobacteria and lactobacilli, which supports digestive health. In food products, it acts as a stabilizer and texturizer, enhancing the shelf life and mouthfeel of dairy and baked goods.

In biotechnology, D-raffinose is employed as a cryoprotectant in the preservation of cells, tissues, and enzymes, helping to maintain structural integrity during freezing and thawing processes. It is also used in culture media for selective microbial growth, particularly in studies involving yeast and fungi, where it helps differentiate metabolic capabilities.

Additionally, D-raffinose finds application in research settings for studying carbohydrate metabolism and enzyme activity, especially in assays involving α-galactosidase. Its low glycemic index makes it suitable for use in dietary products for diabetic nutrition.