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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


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 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.