Gluten-Free Apple Pie Muffins

Gluten-free apple pie muffins are classic muffins that have a moist, tender crumb, and a crunchy topping that makes them stand out. Toasted pecans make all the difference here.

Three gluten-free apple pie muffins on a wooden chopping blocking with parchment paper and white bowls in the background.

Adapted from Katarina Cermelj | Baked to Perfection | Bloomsbury Publishing, 2021

These are best on the day you make them, but you can keep them in a closed container in a cool, dry place for up to 4 days. If you’re serving on days 3 or 4, reheat in the microwave for 5–10 seconds first.–Katarina Cermelj

Apple Pie Muffins FAQs

What is xanthan gum?

Made of fermented corn sugar that’s been dried and powdered, xanthan gum is used extensively in gluten-free foods. Because gluten is what holds baked goods together and provides stretch and strength, gluten-free baking needs something to replicate that.

When using gluten-free flour, always read the label–many flour substitutes already contain xanthan gum, so you might not need to add your own. Too much xanthan gum and your baking may come out heavy or gummy.

How should I store these muffins?

The muffins will keep for a few days at room temperature in a covered container, or can be frozen for longer storage. To freeze, let them cool completely and store in an airtight container or resealable plastic bag. Thaw at room temperature or in the microwave.

Gluten-Free Apple Pie Muffins

Three gluten-free apple pie muffins on a wooden chopping blocking with parchment paper and white bowls in the background.
While these muffins have the most wonderful, moist, cinnamony crumb, dotted with chopped apples, it’s the crumble top that really makes them special. It’s buttery and crunchy, and the chopped pecans get nicely toasted in the oven for an extra layer of flavor.

Prep 1 hr
Cook 25 mins
Total 1 hr 25 mins
12 muffins
369 kcal
5 from 1 vote
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For the cinnamon crumble

  • 2 1/2 ounces (about 1/2 cup) store-bought or homemade gluten-free flour blend
  • 1/4 cup light brown sugar
  • 1/2 teaspoon ground cinnamon
  • 3 tablespoons (1 1/2 oz) unsalted butter cold

For the apple muffins

  • 2 (12 oz) sweet–tart firm apples such as Pink Lady, Granny Smith or Braeburn
  • 2 tablespoons fresh lemon juice
  • 3/4 cup plus 2 tablespoons light brown sugar
  • 1 1/2 teaspoons ground cinnamon
  • 10 ounces (about 2 cups) store-bought or homemade gluten-free flour blend
  • 3 ounces almond flour
  • 2 teaspoons baking powder
  • 1 teaspoon baking soda
  • 1 teaspoon xanthan gum
  • 1/2 teaspoon ground ginger
  • 1/2 teaspoon ground nutmeg
  • 1/2 teaspoon salt
  • 1 stick plus 1 tablespoon (4 1/2 ounces) unsalted butter at room temperature
  • 1/2 cup plus 4 teaspoons whole milk
  • 2/3 cup full-fat plain or Greek yogurt cold
  • 2 large eggs cold
  • 3 1/2 ounces pecans chopped


Make the cinnamon crumble

  • In a small bowl, mix together gluten-free flour blend, sugar, and cinnamon.
  • Add butter and work it into the flour mixture until crumbly but it holds its shape when pressed together.
  • Refrigerate crumble for at least 30 minutes while you prepare the muffin batter. It should be firm or solid to the touch when you sprinkle it on top of the muffins.

Make the apple muffins

  • Adjust an oven shelf to the middle position, preheat oven to 375°F (190°C) and line a 12-hole muffin tin with muffin liners.
  • Peel and core apples, then cube them to about the size of peas.
  • In a medium bowl, toss apple pieces with lemon juice, 2 tablespoons of brown sugar, and 1 teaspoon of cinnamon. Set aside to macerate and release any juices.
  • In the bowl of a fitted with the paddle attachment or a large bowl, sift together gluten-free flour blend, almond flour, remaining 3/4 cup brown sugar, baking powder, baking soda, xanthan gum, remaining 1/2 teaspoon cinnamon, ginger, nutmeg, and salt.
  • Add butter and, using a stand mixer or a fitted with the double beaters, work the butter into the dry ingredients until the texture resembles breadcrumbs or coarse sand, 1 to 3 minutes.
  • In a separate medium bowl, whisk together milk, yogurt, and eggs. Add the wet ingredients to the flour mixture, whisk until batter is smooth, thick, and no flour clumps remain. Fold in chopped apples, any released juices, and 3/4 of the chopped pecans. Divide batter equally between the muffin cups, filling each to the brim.
  • Mix chilled crumble with remaining pecans, and sprinkle on top of muffins. Make sure the majority of the crumble is in a heap in the middle of the muffins with less around the edges, to account for the rise of the muffin top during baking.
  • Bake until an inserted toothpick comes out clean or with a few moist crumbs attached, 25 to 30 minutes.
  • Remove muffins from the tin and place on a wire rack to cool.
Print RecipeBuy the Baked to Perfection cookbook

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Show Nutrition

Serving: 1servingCalories: 369kcal (18%)Carbohydrates: 41g (14%)Protein: 6g (12%)Fat: 22g (34%)Saturated Fat: 8g (50%)Polyunsaturated Fat: 3gMonounsaturated Fat: 7gTrans Fat: 1gCholesterol: 60mg (20%)Sodium: 219mg (10%)Potassium: 160mg (5%)Fiber: 5g (21%)Sugar: 20g (22%)Vitamin A: 395IU (8%)Vitamin C: 1mg (1%)Calcium: 105mg (11%)Iron: 2mg (11%)

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Recipe Testers’ Reviews

While a little on the sweet side and a little more like cake than a muffin or quick bread, these gluten-free apple pie muffins somehow manage to have an incredibly light crumb, and moist, rich flavor at the same time.

Apple Pie Muffin--Deborah W.

The combination of apple-studded muffin with sweet, cinnamon crumble is a reminder that fall is right around the corner and we’re on the cusp of reacquainting ourselves with the flavors of autumn. And for anyone not inclined to try a gluten-free baked good for fear that it will taste odd, these muffins have the lightness and texture of a gluten-full product.

I’ve served these with no accompaniments like butter because they stand on their own for flavor and satisfy a sweet craving without making you feel like you’ve ruined your diet. They take a little while to pull together, but the outcome is well worth the effort.

These gluten-free apple muffins were lovely. They were extremely tender with a nice crumb, good appleness, and a crunchy pecan streusel crumb topping. This is how a muffin should be – if it’s called an apple muffin, I want it PACKED with apple and this one is. 

Apple Pie Muffin--Erin Bloys

My go-to for GF baking, Bob’s Red Mill 1 to 1 Baking Flour, worked its usual magic in this recipe. It rarely disappoints me. The only changes I would make in this recipe are to add a bit of salt into the streusel topping, along with an extra tablespoon of butter to get the topping to have a chunkier texture, and an extra 1/4 tsp salt in the batter. 

Also worth noting, many muffin recipes call for the muffin cup to be 3/4 filled, but this makes quite a lot of batter and because it’s relatively stiff, you can really mound it up above the edge of the muffin cup. This leads to a domed top without a ton of muffin top spread. I hate it when muffins spread and bake together into one giant muffin! My batter was mounded at least an inch in the center above the edge of the cup and they stayed nicely mounded when baked.

These apple pie muffins were my first foray into gluten-free baking and I have to say that I was pleasantly surprised. The tiny bits of apple keep the muffins moist, and the buttery, pecan studded topping gives them a nice crunch. 

A lot of times, muffins can be too sweet. That isn’t the case here. There’s just the right amount of spice, although I may cut the nutmeg in half next time and make up the difference with ground cloves. To me, the nutmeg overpowers the ginger. I didn’t add the xanthan gum because it was already in the flour I used. That was a risk with this being the first time I used gluten-free flour, but it worked out great.

Originally published October 4, 2021


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