By all means, it’s fine to stack your homemade cookies, per Better Homes & Gardens, if they are: sturdy, unfrosted, or have firm-set icing. The cookies from a batter mix that are dropped onto the baking sheet, also known as drop cookies, like chocolate cookies and ginger cookies, for example, can be stacked up. Simply, take the cookies and place them between layers of waxed paper in airtight containers or plastic freezer bags. If the cookies are more fragile, only an airtight container should be used for storage with waxed paper in between layers.
Keep in mind, parchment paper can also be used to divide layers, according to Martha Stewart. The waxed or parchment paper will prevent the cookies from sticking together while also helping them to stay crisp. The experts at Allrecipes even suggest using plastic wrap or tortillas to keep them apart. However, for cookies that aren’t being frozen, metal tins are preferred over plastic containers because they keep the cookies from becoming soft (via Martha Stewart). To avoid worrying about ruined frosting on cookies that have been layered for storage, wait to frost them until you are about to serve them, recommends Southern Living.
Now, if you want to go old school and keep your cookies in an adorable cookie jar, go ahead and place them in, but crispy cookies will do best (per Allrecipes).