The invention provides, in one aspect, a method of making a cocoa-containing food product or ingredient and preserving the levels of a particular polyphenol compound, a collection of polyphenol compounds, and/or total polyphenols present. Certain commonly used baking methods for chocolate cakes and food products use leavening agents that create an alkaline condition that effectively degrades cocoa polyphenols. By monitoring the pH or by adjusting certain alkaline agents or leavening agents used, baked products can be prepared that preserve about 75% or more of the initial cocoa polyphenols present. Food products, cocoa-containing food products, baking mixes and kits, and baked food products produced from the methods are also disclosed.