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Effects of agave fructans as carrier agents on the encapsulation of blue corn anthocyanins using spray-drying were evaluated. Blue corn extract was mixed with 6%, 8%, 10%, and 12% (w/v) of agave fructans in duplicate and dried at 150 °C. The extract showed good contents of anthocyanins, polyphenols, and antioxidant activity. The increase of agave fructans in the encapsulated powders caused a significant increase (p < 0.05) in the humidity, water activity (a_w), pH, bulk density, water solubility index (WSI), and color L* values. On the contrary, the agave fructan addition decreased the hygroscopicity, water absorption index (WAI), antioxidant activity, total anthocyanin, total polyphenol, and individual anthocyanin contents. The encapsulation of blue corn extract with 6% agave fructans (w/v) resulted in good physical, thermal, morphological, and high antioxidant properties. The results suggest that the use of agave fructans as wall material represents advantages in the conservation of anthocyanins and other bioactive compounds from blue corn extract during their encapsulation. The application of blue corn anthocyanin encapsulated powders as a food ingredient is promising for food pigmentation, representing additional advantages for their contribution as a soluble fiber that can benefit the health of consumers.