Additive manufacturing or 3D printing can be applied in the food sector to create food products with personalized properties such as shape, texture, and composition. In this article, we introduce a computer aided engineering (CAE) methodology to design 3D printed food products with tunable mechanical properties. The focus was on the Young modulus as a proxy of texture. Finite element modelling was used to establish the relationship between the Young modulus of 3D printed cookies with a honeycomb structure and their structure parameters. Wall thickness, cell size, and overall porosity were found to influence the Young modulus of the cookies and were, therefore, identified as tunable design parameters. Next, in experimental tests, it was observed that geometry deformations arose during and after 3D printing, affecting cookie structure and texture. The 3D printed cookie porosity was found to be lower than the designed one, strongly influencing the Young modulus. After identifying the changes in porosity through X-ray micro-computed tomography, a good match was observed between computational and experimental Young’s modulus values. These results showed that changes in the geometry have to be quantified and considered to obtain a reliable prediction of the Young modulus of the 3D printed cookies.