Disclosed are sterilized, aseptically packaged, liquid nutritional formulas, and corresponding methods of making the formulas, wherein the formulas comprise Vitamin D and extensively hydrolyzed protein having a degree of hydrolysis of at least about 20%, and wherein the packaged formula is prepared by (a) sterilizing a liquid nutritional formula containing Vitamin D and extensively hydrolyzed protein having a degree of hydrolysis of at least about 20%; (b) sterilizing a container; and then (c) aseptically packaging the sterilized liquid nutritional formula in the sterilized container. The packaged formulas exhibit improved Vitamin D stability.