A system generates a secure barcode by: identifying a primary pattern for a two-dimensional barcode to be printed on a substrate, wherein the primary pattern comprises of a set of dark cells and a set of light cells; identifying a two-dimensional micro-shape, wherein the micro-shape has a size that is no larger than a size of each cell of the two-dimensional barcode; generating a secondary pattern comprising a plurality of the micro-shapes; and superimposing the secondary pattern with the primary pattern for the two-dimensional barcode to yield a secure barcode. The resulting two-dimensional barcode includes a primary pattern comprising a set of dark cells and a set of light cells, where the sets represent encoded data, along with a secondary pattern of micro-shapes that are superimposed with the primary pattern.