Abstract: The stack height and moisture content of baked goods produced continuously in a multi-zone oven, such as a gas-fired band oven, is controlled and adjusted using microwave energy. Color development, flavor development, texture, and appearance of the baked products are not adversely affected by the replacement of a substantial amount of the non-microwave energy input with microwave energy. The stack height and moisture content of the baked product may be controlled or adjusted with the microwave energy to be within predetermined ranges or specifications independently of each other. Upon detection of product which is not within specifications, the microwave energy may be used to rapidly adjust stack height and/or moisture content so that they quickly return to their predetermined acceptable levels thereby substantially reducing product waste or recycling. The stack height of the baked pieces is controlled and adjusted using microwave energy early in the baking process.