Published February 1, 2005. From Cook's Illustrated.
What’s the best way to keep cookies fresh?
When it comes to storing cookies, too much air exposure dries them out and causes staling. To find the best method for storing chewy cookies (which typically suffer more from age than crispy cookies), we baked three types—chocolate chip, molasses spice, and peanut butter—and stored them the following ways: in a zipper-lock bag with the air pressed out; in a zipper-lock bag with an apple slice; and in a zipper-lock bag with a slice of white sandwich bread thrown in. We tried the bread since sugar (in the cookies) is by nature highly hygroscopic, meaning that it attracts moisture and will thus absorb it from surrounding sources, like an apple slice or bread.
After five days, all three cookie samples exhibited negative traits. The ones simply placed in the bag had become dry on the edges but were still acceptable. Those stored with the apple slice were moist but had begun to pick up the odor and flavor of the apple. The cookies stored with a slice of bread became surprisingly damp in the areas where the bread touched the cookies. We thought less bread might work and tested smaller amounts, but to no avail. So, in the end, the best way to store cookies is also the simplest: in a zipper-lock bag with the air pressed out.
Stored cookies can also be “refreshed” to just-baked chewiness. Simply place them on a microwave-safe plate and microwave at full power for 30 seconds or bake them at 425-degree oven for four to five minutes. Make sure to let the cookies cool on the baking sheet for a couple of minutes before removing them, and consume them while they're warm.
For long-term cookie storage, we recommend freezing. That being said, we’ve noticed an unwanted crunchiness when comparing fresh-baked cookies against those that have been frozen and thawed at room temperature. After doing some research, we learned that sugars become significantly more crystalline (less likely to dissolve) as the temperature drops. In the freezer, then, the extremely low temperature causes the sugars to begin to come out of solution and recrystallize and hence the crunchiness. We found that this can be simply remedied by a little heat--either four or five minutes in a 350-degree oven or microwaved on full power for 30 seconds. Once cooled to room temperature, they were nearly as good as their fresh counterparts: chewy and crystal-free.