The Danish buttered cookie is a famous confectionery product. Its success makes manufacturing of the large volumes required challenging, introducing the need for different strategies to increase production while maintaining a high-quality standard. Two manufacturing lines used are batch-wise and continuous dough mixing. Despite the recipe being the same, the outcome of the two production types differs in texture and external appearance. While this does not infringe on the quality, changes in texture are observable. This manuscript analyses the physicochemical differences of the cookies after baking using Near Infrared hyperspectral imaging and Chemometrics. The study demonstrates that the changes in texture between batch and continuous production are mostly due to the difference in crystalline sucrose emerging in invisible spots on or near the surface of the cookies and a higher tendency of migrated butter-fat spots on the surface of the cookies for the continuous manufacturing procedure.