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Apple pie cupcakes capture everything cozy about apple pie in a handheld, grain-free cupcake. Applesauce flavors both the tender crumb and the thick filling hidden inside, and caramel icing crowns the top. They came from watching a bakery punch and fill cupcakes on a rainy afternoon — and they work.
Pro Tips
- Use thick applesauce for the filling — if you're using a runny store-bought brand, simmer it uncovered on the stovetop for a few minutes first or it will leak out the bottom of the cupcake.
- Cool the cupcakes thoroughly before coring; an apple corer makes clean wells, but stop before you punch through the paper liner.
- Fill the cored centers with a piping bag or squeeze bottle until the sauce is just level with the top of the cupcake — overfilling makes the caramel icing slide off.
- Fill the lined cups ¾ full and bake at 350 degrees for about 25 minutes, until the centers are firm rather than soft.
- Store them chilled for up to a week — the applesauce filling keeps the crumb moist the whole time.
Frequently Asked Questions
Can I use store-bought applesauce?
Yes, but thicken it first: cook it uncovered in a pan for a few minutes until it mounds on a spoon. Thin sauce is the number-one cause of soggy, leaking cupcakes.
How far ahead can I make apple pie cupcakes?
Up to a week if you store them chilled. The filling and caramel icing hold up so well that they're ideal for baking on the weekend and eating all week.
What's the topping on these cupcakes?
Caramel icing, spread over the filled cupcake. It plays perfectly against the applesauce filling and finishes the apple-pie impression.
Do I have to core and fill them?
They're lovely as plain applesauce cupcakes, but the hidden filling is the whole fun — it's what turns them into a pocket of apple pie.
Recipe Card

Ingredients
Method
- 1.
- Beat together ½ cup applesauce with oil and honey.
- 2.
- Add eggs and vanilla while beating the wet mixture.
- 3.
- In a separate bowl, sift and combine the flours, baking soda, and salt.
- 4. Slowly add the dry ingredients to wet ingredients, while beating on low, until just combined.
- 5. Fill lined muffin cups ¾ full and bake at 350 degrees for 25 minutes, or until centers are firm.
- 6. Use an apple corer to remove the center of the thoroughly cooled cupcakes, careful not to punch through the liner.
- 7. Use piping bag or squeeze bottle (save those empty containers!) to fill the cored portion of the cupcake with thick applesauce, until just level with the cupcake.
- 8.
- Top with Caramel Icing.
- 9. Store chilled for up to a week.




