The objective of this research was to understand the effects of baking in an industrial tunnel oven on the physicochemical properties of commercially formulated short-dough cookies. Quality parameters of the cookies, including moisture content, dimensions and color were tracked throughout baking. Instrumental evaluations of compression and fracturability, acrylamide concentration and proton mobility were conducted and used to explain the changes that occurred. Peak acrylamide values were observed after L* values dropped, suggesting there may be a point at which color development and low acrylamide values overlap, allowing for optimization of color and lower acrylamide content. Pasting properties of cookies as measured by RVA showed few differences. Baking resulted in a loss of birefringence in a subset of A-type starch granules providing some evidence of starch granule damage. Proton mobility decreased during baking as moisture loss progressed and interactions between starch and water increased. Isolation of starch from the treatments however demonstrated few differences in crystallinity, pasting behavior or gelatinization enthalpy. Characterization of these product parameters and process variables could suggest strategies for altering a commercial process to modulate quality and also develop strategies to reduce energy consumption.