Gluten Free Apple Muffins Recipe
Tall apple muffins with cinnamon and a buttery crumb topping, made gluten free. This version is made with a 1 to 1 gluten free flour blend, and nobody at the table will guess.

Gluten Free Apple Muffins That Taste Like the Real Thing
Every recipe on Everything Muffins starts in our kitchen and finishes in yours. Our team of bakers developed these gluten free apple muffins batch by batch, testing apple varieties and gluten free blends until the crumb was soft and the apples stayed juicy. Then we shared the recipe with our community of home test bakers, who made it in their own kitchens with their own ovens, pans and ingredients.
What they told us went straight into the recipe below. In Test #1, the smell of cinnamon and apple baking was pure fall before the pan even came out.
Why You’ll Love This Recipe
- Buttery crumb topping: Brown sugar and cinnamon crumbs bake into a crunchy top.
- Gluten free, not gritty: A 30 minute rest lets the gluten free flour hydrate for a soft, tender crumb.
- Community tested: Our bakers built it, then home bakers tested it in their own kitchens before it went live.
Ingredients You’ll Need
Full amounts are in the recipe card below. Here’s what each ingredient does and what you can swap.
- Gluten free flour: a 1 to 1 baking blend with xanthan gum already in it. Weigh it if you can, since blends vary.
- Brown sugar: caramel flavor that pairs with apple and cinnamon.
- Baking powder and baking soda: baking powder does most of the lifting, and the soda helps the tops brown.
- Eggs: two, at room temperature, for rise and structure.
- Sour cream, milk and oil: oil keeps gluten free muffins moist longer. Greek yogurt works in place of sour cream.
- Apples: Honeycrisp, Gala or Fuji, peeled and finely chopped.
- Crumb topping: brown sugar, flour, cold butter and cinnamon.
How to Make Gluten Free Apple Muffins Recipe
Step 1: Make the batter
Toss the finely chopped apple with a spoonful of the flour mixture, plus another 1/2 teaspoon of cinnamon if you want extra cinnamon flavor. Whisk the wet ingredients, fold into the dry ingredients and fold in the apples. Pinch the crumb topping ingredients together until clumpy.
Baker’s Tip: Chop the apple fine, about 1/8 inch, so it softens as it bakes and does not sink.
Step 2: Rest and fill
Let the batter rest for 30 minutes while the oven heats. Then use a large cookie scoop or 1/3 cup measure to fill all 12 liners to the top.
Tester Tip: A 15 minute rest left the crumb a little grainy in Test #1, so rest the batter at least 20 minutes, and use the full 30 for the softest texture. The batter fills the liners very full without spilling over. Paper liners grabbed these muffins, so give them a light coat of oil spray or use parchment liners.
Step 3: Bake
Bake at 400°F for 5 minutes, then lower the oven to 350°F without opening the door and bake 16 to 19 minutes more.
They’re done when the tops spring back, a toothpick comes out clean and the centers read 200 to 205°F.
What Our Test Bakers Learned
Before a recipe goes live, our community bakes it and reports back. Here’s what they found and what we changed because of it.
- What testers changed or asked about: In Test #1, the texture and fluffiness were great once the rest was long enough. The tasters suggested tossing the finely chopped apple with an extra 1/2 teaspoon of cinnamon before folding it in, and the muffins stuck to paper liners until they were lightly sprayed.
Tips for Perfect Muffins Every Time
- Weigh your flour, or spoon it into the cup and level it. Extra flour makes thick batter and dense muffins.
- Use room temperature eggs and dairy. Set eggs in warm water for 5 minutes if you forget.
- Do not open the oven when you lower the temperature. That first blast of heat is what gives you tall tops.
- Check your oven with an oven thermometer. Many ovens run hot or cold.
- Dark pans bake faster, so start checking 2 to 3 minutes early.
- Gluten free muffins taste best the day they are baked. Warm leftovers for 10 seconds in the microwave to soften them.
- Let the muffins cool completely before peeling the wrappers. Warm muffins steam against the paper and cling to it, but once fully cooled the wrappers release cleanly.
Storing and Freezing
Store cooled muffins in an airtight container at room temperature for up to 2 days, or in the fridge for up to 5 days. To freeze, wrap them individually and freeze for up to 3 months. Thaw overnight or warm in the microwave for 15 to 20 seconds.
Frequently Asked Questions
Yes. Peel the apples before chopping so there is no tough skin in the finished muffins.
Honeycrisp, Gala and Fuji stay sweet and hold their shape.
Yes. Sprinkle with cinnamon sugar instead.
A 1 to 1 baking blend that already has xanthan gum. Skip almond or coconut flour on their own, they need a different recipe.

Easy Gluten Free Apple Muffins
Ingredients
Method
- Preheat the oven to 400°F. Line a 12 cup muffin pan with parchment liners, or lightly spray paper liners with oil so the muffins release cleanly.
- In a large bowl, whisk together the gluten free flour, packed brown sugar, baking powder, baking soda, salt, cinnamon and nutmeg. Set aside.
- In a medium bowl, whisk the eggs, sour cream, milk, oil and vanilla until smooth.
- In a small bowl, pinch together the crumb topping ingredients with your fingers until clumpy. Set aside.
- Pour the wet ingredients into the dry ingredients and gently fold just until no dry flour remains. Fold in the finely chopped apples, tossed with an extra 1/2 tsp cinnamon if you like. Do not overmix. Let the batter rest for 30 minutes (never less than 20) before scooping so the gluten free flour can hydrate.
- Use a large cookie scoop or 1/3 cup measure to divide the batter evenly among the 12 liners, filling them to the top. Sprinkle the crumb topping over the batter.
- Bake at 400°F for 5 minutes. Without opening the door, lower the oven to 350°F and bake 16 to 19 minutes more, until the tops spring back, a toothpick in the center comes out clean and the center reads 200 to 205°F.
- Cool in the pan for 5 minutes, then move the muffins to a wire rack. Let them cool completely before peeling off the liners.
Notes
| Calories | 307 |
|---|---|
| Total fat | 14 g |
| Saturated fat | 4 g |
| Cholesterol | 42 mg |
| Sodium | 281 mg |
| Total carbohydrate | 43 g |
| Fiber | 1 g |
| Sugars | 21 g |
| Protein | 2 g |
