You thought the muffins were done. After all, they were golden-brown on the tops, but when you cut into one, it's still doughy. Get them back into the oven fast. The sooner you notice the problem, the more successful you'll be in fixing it.
Into the Oven
Muffins are soft when they first come out of the oven, but the dough shouldn't be raw. If you see mushy, uncooked portions in the muffins, put them back in the tins. Slide them into the oven for an additional 5 to 10 minutes, or until a toothpick inserted in the centers comes out clean, with just a few moist crumbs. Watch them closely because they'll dry out if you cook them too long. Because undercooked muffins contain raw eggs, rebake them within 2 hours. After that, bacteria in the raw eggs may begin to grow, potentially causing foodborne illness.
A Sinking Feeling
If you took the muffins out before the sides and tops were set, they may collapse inward. Baking them again will firm them, but it won't fix a sunken appearance. Another reason muffins might collapse is that you didn't use enough leavener or the leavener wasn't fresh. In general, use 1 teaspoon baking powder or 1/4 teaspoon baking soda for each cup of flour in a muffin recipe. Store both leaveners in a dry, cool pantry and replace baking powder every six months. Baking soda stays fresh for at least one year.
In the future, save yourself some trouble by making sure the muffins are cooked completely the first time. Preheat the oven for at least 10 to 15 minutes at 375 or 400 degrees Fahrenheit. Place the muffins on the middle rack and don't overcrowd them. Two muffin tins is about all most home ovens can handle at one time. Set the timer for 5 minutes before you think they'll be done. Stick a toothpick in the muffins. The toothpick should come out clean. A wet or sticky toothpick means the muffins aren't done yet. When done, the muffins should spring back lightly to your touch. Don't wait until the muffins are pulling away from the sides of the pan. By this time, they're usually overbaked. Cover the muffins loosely with foil if the tops are browning too quickly.
Take Its Temperature
If you've made all the necessary corrections but your muffins still aren't baking correctly, the problem might be your oven. Oven temperatures -- even in new ovens -- can be off by as much as 50 to 100 degrees. This variation can cause major kinks in your baking success. Place an oven thermometer in the oven to check its accuracy. If the oven is off -- either too hot or too cool -- simply adjust the temperature in the future. If the oven is too hot, turn the temperature down. If it's too cool, turn the temperature up.