These gluten-free apple muffins are the sleeper hit I keep coming back to. Bakery-style, extra moist, and packed with chunky fresh apples in every bite – what’s not to love? The secret to a tender, fluffy crumb that never dries out is all about the yogurt (or sour cream) and butter combo. A clumpy, buttery cinnamon brown sugar crumb topping finishes them off, and for those of you feeling it – drizzle a sweet vanilla glaze on top.

an apple muffin on a blue and white plate with a bite taken out
My homemade gluten-free apple muffin recipe is better than bakery-style! Tall, floofy, never dry, loaded with fresh apple chunks, with a sugary, clumpy crumb topping bonus.

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(Finally) Homemade Gluten Free Apple Muffin Recipe Win

With fall approaching, I wanted to take advantage of the peak apple season. What is a better way than a warm, cinnamon-spiced gluten-free apple muffins recipe? They are my unexpected hit within tons of gluten-free muffin ideas. No one dreams a GF apple muffin to have a better taste and texture than anything they remember. #winning

Instead of using applesauce to flavor the muffins, the cinnamon batter is laced with lots of chunky apple bites. The soft, tender interior is topped with a thick crumb topping, held together with clumps of sweet glaze oozing in all the crevices.

Recipes like my apple muffins and legendary butterscotch gluten-free apple scones use a butter and sour cream (or yogurt) mixture to coat the gluten-free flour starches. The crumb stays soft and moist, never dry or crumbly. Using a mix of fat, rather than all oil or butter, adds moisture, but doesn’t risk weighing down the texture to something dense and oily.

For the crumb topping I borrowed a GF baking trick from my vintage-style gluten-free crumb coffee cake. Adding an yolk to the streusel topping helps bind the brown sugar crumbs together, avoiding a sandy, gritty streusel on top.

If you’re in need of a dairy-free recipe, the yogurt can be swapped out with either a non-dairy yogurt or sour cream. As for the butter, I prefer this over a neutral tasting oil, but this can also be replaced with a dairy-free substitute.

Thanks, very easy to make. They were very moist which is hard to find in a gluten-free recipes. My husband said, “These are the best muffins I’ve ever eaten.”

—MMill

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Let’s Make This Together!

Want to save time and an extra step? Feel free to forgo the crumb topping, or do a simple sprinkle of coarse sugar on top for a crunchy, sweet finish.

(Below shows step-by-step photos and modified instructions. For the complete recipe, along with ingredient amounts, scroll down to the recipe card.)

Fluffy muffin batter starts with creamed butter

For the apple muffin batter in a large mixing bowl beat together the softened butter, brown sugar, and sugar until very light and fluffy, about 2-3 minutes. Mix in the yogurt or sour cream, eggs, and vanilla to combine well.

adding the eggs and yogurt to the butter sugar.
When creaming butter and sugar, don’t stop as soon as it’s blended. Continue beating at high speed until it’s pale, light, and fluffy, which takes a few minutes.

Dry ingredients and fresh apples

Next, add the dry ingredients to the wet ingredients – gluten-free flour, baking soda, baking powder, cinnamon, and salt. Finally, mix in the chopped apples on low speed.

adding fresh apples to the muffin batter.
Peel and dice the apples in small chunks to get loads of juicy bits in every bite.

Secret to a moist crumb topping, never dry or sandy

For the topping combine the dry ingredients – brown sugar, gluten-free flour, and cinnamon. Stir in the melted butter and egg yolk until well combined. The egg yolk acts as an extra binder, so the streusel clumps together. GF flour can be very gritty and we don’t want to ruin a perfectly moist muffin with a bad finish!

crumb topping for apple muffins.
Yes, the cinnamon crumb can be left off, but boy does it make these fresh apple cinnamon muffins glorious!

Sprinkle and bake

Divide the batter in the muffin pan, filling all the way to the top. I like to use a large trigger scoop to do this quickly and evenly. Break off chunks of crumb topping and press gently on top to flatten evenly

Bake for about 18-20 minutes, rotating halfway through. Test with a toothpick to make sure the muffins are cooked through under the topping. Transfer muffins to a cooling rack and drizzle with glaze, if desired.

unbaked muffins with crumb topping.
It will seem like a lot of muffin batter in each cup, but we are going for full bakery-style vibes here. Tall, domed and swoon-worthy!

Wondering what the best variety of fresh apples are to bake with? For a tarter balance to the sweetness, use Granny Smith. For a sweeter apple, my preferred are Golden Delicious or Honey Crisp. I would avoid using Red Delicious or Gala because they break down too much during baking.

Make GF Apple Muffins Extra Yummy

Don’t get me wrong, my apple muffins have a lot going on and won’t leave you wanting, but I have a hard time not dreaming up new versions every time I make them.

I love the combo of apple cinnamon with butterscotch or white chocolate chips. Just be sure to read the ingredient label because some baking chips aren’t safe for a GF diet.

Of course, adding chopped nuts, such as walnuts or pecans are always a delish option. If you’d like, you can even work in a few tablespoons into the streusel topping.

a gluten-free apple muffin partially unwrapped from a paper liner
The vanilla glaze topping ties it all together. It drizzles between the brown sugar clumps, holds it all together, and is a creamy balance to the fresh apples.

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an apple muffin on a blue and white plate with a bite taken out
4.78 stars (22 ratings)

Tender, Moist Gluten-Free Apple Crumb Muffins

Melissa Erdelac of MamaGourmand headshot in patterned dress.Melissa Erdelac
Yield: 12
Prep Time: 10 minutes
Cook Time: 18 minutes
Total Time: 28 minutes
These gluten-free apple muffins are the sleeper hit I keep coming back to. Bakery-style, extra moist, and packed with chunky fresh apples in every bite – what's not to love? The secret to a tender, fluffy crumb that never dries out is all about the yogurt (or sour cream) and butter combo. A clumpy, buttery cinnamon brown sugar crumb topping finishes them off, and for those of you feeling it – drizzle a sweet vanilla glaze on top.
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Ingredients
 

Gluten-Free Apple Muffins

Crumb Topping

Vanilla Glaze (optional)

Equipment

Instructions
 

  • Preheat the oven to 375°F. Liberally grease 12 muffin cups with nonstick cooking spray or line with paper cups.
  • In a large bowl beat together the softened butter, brown sugar, and sugar until pale, light and fluffy, about 2-3 minutes.
    ½ cup unsalted butter, ½ cup packed light brown sugar, ¼ cup granulated sugar
  • Add in the yogurt or sour cream, eggs, and vanilla to mix until very well combined.
    2 large eggs, ½ cup yogurt or sour cream, 2 teaspoons vanilla extract
  • Add the gluten-free flour, baking soda, baking powder, cinnamon, and salt. Combine on medium-low speed until no flour pockets remain. Finally, mix in the chopped apples on low speed.
    1 ¾ cup gluten-free all purpose flour, 1 teaspoon baking soda, 1 teaspoon baking powder, 1 teaspoon cinnamon, ½ teaspoon salt, 2 cups peeled and chopped apples
  • Divide the batter between the muffin tins, filling all the way to the top. It will seem like a lot of batter for each muffin tin, but it works! Set that aside so the GF starches soften and hydrate while the crumb topping is prepared.
  • For the crumb topping, in a medium bowl combine the flour, brown sugar, and cinnamon. Stir in the melted butter and egg yolk until well combined.
    ½ cup gluten-free all purpose flour, ⅓ cup packed light brown sugar, ½ teaspoon ground cinnamon, 3 tablespoons unsalted butter, 1 egg yolk
  • Break off chunks of crumb topping until evenly divided on top, pressing down slightly. Bake for 18-20 minutes, rotating halfway through. Insert a toothpick, beyond the crumb topping into the muffin, to make sure it comes out without any wet batter.
  • Cool the muffins in the pan for 5 minutes then gently pop out onto a wire rack to cool. For the glaze, whisk together all the ingredients and drizzle on top. Let the glaze harden before storing.
    1 cup powdered sugar, 1 ½ tablespoon milk or cream, ½ teaspoon vanilla extract

Notes

Storing
Store at room temperature in an airtight container up to 2 days. Refrigeration is not recommended because it will dry them out. To freeze, make sure they have cooled completely and wrap each muffin in plastic wrap for best results. Transfer the muffins to a ziplock freezer bag and freeze up to 3 months.
 
Recipe adapted from Sally’s Baking Addiction
Calories: 317kcal, Carbohydrates: 49g, Protein: 4g, Fat: 13g, Saturated Fat: 7g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 3g, Trans Fat: 1g, Cholesterol: 73mg, Sodium: 302mg, Potassium: 111mg, Fiber: 3g, Sugar: 32g, Vitamin A: 410IU, Vitamin C: 1mg, Calcium: 68mg, Iron: 1mg
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