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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


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.

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.

Katarina Cermelj

Prep 1 hr

Cook 25 mins

Total 1 hr 25 mins



12 muffins

369 kcal

No ratings yet

For the cinnamon crumble

For the apple muffins

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 stand mixer 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 hand mixer 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.

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%)

Recipe Testers’ Reviews

Originally published October 4, 2021



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