Apple Cinnamon Muffins (gluten-free option)

Glazed muffins with kanzi apples on a wooden board.
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5 from 3 reviews

This easy recipe makes the best apple cinnamon muffins, filled with warm spices and juicy chunks of fruit, and dripping with a sweet apple cider cinnamon glaze. They're so moist and tender that you'd never know they're gluten-free. If you start baking them now, they can be in your oven in under 30 minutes!

  • Author: Alexandra
  • Prep Time: 35 minutes
  • Cook Time: 15 minutes (up to 20 minutes)
  • Total Time: 50 minutes (up to 55 minutes)
  • Yield: 12 muffins 1x
  • Category: muffins
  • Method: baking
  • Cuisine: American
  • Diet: Gluten Free



Gluten-Free Apple Cinnamon Muffins

  • 3 ounces (6 tablespoons) unsalted butter, sliced
  • 6 3/8 ounces (2/3 cup plus 3 tablespoons, packed) brown sugar, divided use
  • 3 teaspoons ground cinnamon, divided use
  • 12 5/8 ounces (2 2/3 cups) peeled and finely chopped apples (about 2 medium-large)
  • 10 5/8 ounces (2 1/2 cups, spoon and level) gluten-free all-purpose flour with xanthan gum
  • 1 tablespoon baking powder
  • 1/2 teaspoon salt
  • 1/4 teaspoon ground nutmeg
  • 1/4 teaspoon ground allspice
  • 4 ounces (1/2 cup) coconut oil, melted
  • 2 large eggs
  • 6 ounces (3/4 cup) whole milk Greek yogurt
  • 1 tablespoon vanilla extract

Apple Cinnamon Glaze

  • 4 1/2 ounces (1 1/8 cups) confectioner's sugar, sifted
  • 2 1/4 tablespoons apple cider or apple juice
  • 1 1/2 tablespoons unsalted butter, melted
  • 1 1/2 teaspoons vanilla extract
  • 3/4 teaspoon ground cinnamon
  • heavy pinch of salt
  • dash of ground nutmeg
  • dash of ground allspice


Spiced Apple Muffins

  1. Oven and pan prep: Preheat oven to 375ºF and grease a standard 12-cup muffin pan with nonstick spray.
  2. Cook the apples: Melt the butter in a large skillet over medium-low heat. Whisk in 3 tablespoons of brown sugar and 2 teaspoons of cinnamon and cook for another 30 seconds, stirring constantly. Add sliced apples, stirring to coat. Cook for 5-10 minutes, stirring occasionally, until apples are tender. Remove from heat and set aside.
  3. Mix dry ingredients: Meanwhile, in a medium mixing bowl, whisk together the gluten-free all-purpose flour, baking powder, salt, nutmeg, allspice, and remaining 1 teaspoon cinnamon.
  4. Mix wet ingredients: In a separate, large bowl, whisk together the melted coconut oil and brown sugar until combined. Beat in the eggs one at a time, until thick and smoothly emulsified. Whisk in the yogurt and vanilla until fully incorporated.
  5. Combine: Add the dry ingredients to the wet and fold in just until mostly incorporated - batter will be thick. Strain any extra juice from the cooked apples, reserving for glaze if possible (see notes). Add the apples to the batter and fold in everything is evenly incorporated and the apples are dispersed.
  6. Portion and bake: Divide the batter evenly between the prepared muffin cups (they will be nearly full), using your fingertips to lightly smooth out the tops of the muffins as needed. Bake at 375ºF for 5 minutes, and then reduce heat to 350º and bake about another 10-15 minutes, until a toothpick inserted into the center of one comes out clean. Cool in pan for 5-10 minutes, and then transfer to a wire rack to cool completely before glazing.

Apple Cinnamon Glaze

  1. Make the glaze: In a small mixing bowl, combine all ingredients for the glaze: sifted confectioner's sugar, apple cider/juice, melted butter, vanilla extract, cinnamon, salt, nutmeg, and allspice. Whisk together until smooth. The glaze should be just thick enough to drizzle over the muffins in a thin layer; you can add more confectioner's sugar if needed. 
  2. Drizzle over muffins: Spoon glaze over each muffin, allowing to drizzle down sides and set.


Ingredient notes and substitutions:

  • To use salted butter, I would suggest dialing back the added salt in the muffins to 3/8 teaspoon  and skipping the salt in the glaze.
  • I used Kanzi apples for these muffins, but any variety with a crisp texture, and preferably a nice sweet-tart balance, will work well. A few suggestions: Empire, Pink Lady, Fuji, Honeycrisp, Juici, Gala, or Braeburn. 
  • Regular all-purpose flour can also be used in place of gluten-free flour. 
  • In place of the coconut oil, you can use any neutral-flavored cooking oil.
  • While I recommend a whole milk Greek yogurt, any plain Greek yogurt - or even sour cream - should do the trick. 
  • If you have enough reserved juices from cooking the apples, you can use this in place of the cider/juice in the glaze. Boiled cider would also be ideal, but you can even use milk in a pinch. 

Storage and shelf life: 

  • I recommend storing these muffins in an airtight, zip-top bag or container. They'll keep well (and stay moist) at cool room temperature for up to a few days, but should be refrigerated for longer storage (5-7 days) since they contain fresh fruit. If refrigerated, I suggest letting them come to room temperature or microwaving briefly before serving. They would likely freeze well if unglazed; wrap individual muffins in plastic wrap and store in an freezer-safe bag or container.