If you are planning to freeze back some of your muffins, here is a very simple way to freeze muffins. Allow your cooked muffins to fully cool. Then transfer into a freezer container or freezer bag. Place muffins in the freezer for up to three months. Thaw on the counter or in the fridge. Or toss frozen muffins right in the microwave and do a 15-second heat-up, until the muffins are fully warmed. It gives that fresh out of the oven warmth!