Gluten Free Apple Muffins Recipe

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My easy gluten free apple muffins make the perfect fall breakfast! They’re easy to make, delicious and so moist!

Gluten free apple muffin on a white dessert plate in front of the cooling rack full of more muffins.

Every fall, my daughters and I go into baking mode. It’s a great way to kick off apple season together!

One of our favorite quick breakfast recipes to make are these gluten-free apple cinnamon muffins. I never knew you could make such moist muffins that are gluten free until I perfected this simple recipe!

Best of all, you only need basic ingredients like fresh apples, a gluten free flour blend, butter, sugar, eggs and spices to make these delicious gluten-free muffins.

Ingredients

Ingredients for gluten free apple muffins measured out into bowls to make the baking process easier.
  • 2 eggs
  • ¾ cup of granulated sugar
  • ½ cup of melted butter
  • ⅔ cup of applesauce
  • 1 ½ cups of gluten free all purpose flour
  • 1 teaspoon of baking powder
  • ½ teaspoon of baking soda
  • 1 teaspoon of ground cinnamon
  • 1 teaspoon of pumpkin spice
  • 1 cup of grated apple

Equipment

  • Measuring cups and spoons
  • Mixing bowls
  • Whisk
  • Grater or food processor
  • Muffin tin for 12 muffins
  • 12 paper muffin liners

By the Numbers: How to Make Gluten Free Apple Muffins

Follow these simple step-by-step instructions to learn how to make the absolute best apple muffins that are gluten free!

Step 1: Preheat Oven & Prepare Pan

Preheat oven to 350˚ F. Line your cupcake pan with paper liners. You’ll need 12.

Muffin pan lined with 12 brown paper liners.

Step 2: Combine Liquid Ingredients

In a large mixing bowl, whisk together 2 eggs, ¾ cup of sugar, ½ cup of melted butter and ⅔ cup of applesauce.

Butter, applesauce, sugar and eggs being whisked together in a large glass mixing bowl.

Step 3: Combine Dry Ingredients

In a separate mixing bowl, combine 1 ½ cups of gluten free flour, 1 teaspoon of baking powder, ½ teaspoon of baking soda, 1 teaspoon of cinnamon and 1 teaspoon of pumpkin spice.

Gluten free flour mixture being stirred in a glass mixing bowl.

Step 4: Mix Dry with Wet Ingredients

Add the dry mixture to the wet mixture and whisk until everything is well combined.

Gluten free apple muffin batter being whisked together in mixing bowl.

Step 5: Add Grated Apple

Next, gently fold in 1 cup of fresh, grated apple.

Grated apple being folded into gluten free muffin batter.

Step 6: Fill Muffin Tin

Fill your paper liners with your cupcake mixture until they’re almost full. This muffin batter will fill 12 cups perfectly.

Gluten free apple muffin batter scooped into muffin tin.

Step 7: Bake Apple Muffins

Place the muffin pan in the oven and bake for 22-25 minutes or until a toothpick comes out clean.

Baked gluten free apple muffins cooling in the pan.

Step 8: Cool Muffins

Once done, remove the pan from the oven and allow the muffins to cool for about 5 minutes in the pan before transferring them to a wire rack to cool to room temperature.

Gluten free apple muffins cooling on a wire rack.

Step 9: Eat Muffins

Allow your muffins to cool completely, then enjoy your Gluten Free Apple Muffins.

Gluten free apple muffins served on a white dessert plate; set next to the cooling rack of more muffins.

Tips for Making the Best Gluten Free Apple Muffins

Answers to all of your questions about making this delicious gluten-free apple muffin recipe, including tips and substitution ideas.

Best apples

You can use any kind of apples you can pick from a tree or buy from the grocery store. Some popular choices for sweet apples are pink lady, gala and honeycrisp apples. If you prefer tart apples, you can use granny smith but the muffins won’t be as sweet.

Best gluten free flour

I most often use Bob’s Red Mill in this recipe, but you can typically get away with most gluten free flour blends that contain xanthan gum when making muffins.

Dairy-free option

Replace the butter with refined olive oil, vegetable oil, melted coconut oil or your favorite neutral oil.

Vegan option

In addition to substituting oil for butter, you’ll also need to replace the eggs with a vegan substitute. Flax eggs tend to work well in muffins.

Chunkier muffins

If you like apple chunks in your muffins, you can use half diced apples and half grated apples. For best results, I don’t recommend replacing all of the grated apples with chopped apples or they won’t bind together as well.

Storage tips

Store your leftover muffins in the fridge in an airtight container for up to 4 days. They’ll also last about 2 days at room temperature.

Or you can wrap them each tightly in plastic wrap, freeze them individually, then store them in a freezer bag. That way you can defrost and enjoy one at a time.

Free gluten free baking guide

If you’re new to gluten-free baking, sign up for my free guide:

7 Secrets to Gluten Free Baking

3 slices of homemade gluten free bread on cutting board.

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More gluten free muffin recipes

Need recipes for more gluten free muffins that can be enjoyed as a quick breakfast? Try these options:

More gluten free apple recipes

If you have an abundance of apples, try some of these delicious gluten-free recipes:

Two gluten free apple muffins; one sliced in half and one whole.

Gluten Free Apple Muffins

Learn how to make the best gluten-free apple muffins. It’s a great recipe for grab-and-go breakfasts in the fall.
5 from 1 vote
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Prep Time: 15 minutes
Cook Time: 22 minutes
Total Time: 37 minutes
Recipe Servings: 12

Ingredients

  • 2 eggs
  • ¾ cup granulated sugar
  • ½ cup butter - melted
  • cup applesauce
  • 1 ½ cups all purpose gluten free flour - that contains xanthan gum
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • 1 teaspoon ground cinnamon
  • 1 teaspoon pumpkin spice
  • 1 cup fresh apple - grated

Equipment

Instructions

  • Preheat oven to 350˚ F. Line your cupcake pan with paper liners.
    Muffin pan lined with 12 brown paper liners.
  • Whisk together the eggs, white sugar, melted butter and applesauce in a large bowl.
    Butter, applesauce, sugar and eggs being whisked together in a large glass mixing bowl.
  • In a another bowl, combine gluten-free flour, baking powder, baking soda, cinnamon and pumpkin spice.
    Gluten free flour mixture being stirred in a glass mixing bowl.
  • Add the flour mixture to the wet ingredients and whisk until combined.
    Gluten free apple muffin batter being whisked together in mixing bowl.
  • Fold in the grated apple.
    Grated apple being folded into gluten free muffin batter.
  • Scoop batter into your muffin cups until they’re almost full.
    Gluten free apple muffin batter scooped into muffin tin.
  • Bake for 22-25 minutes or until a toothpick comes out clean.
    Baked gluten free apple muffins cooling in the pan.
  • Remove the pan from the oven and allow the muffins to cool for about 5 minutes before transferring them to a cooling rack.
    Gluten free apple muffins cooling on a wire rack.
  • Allow your muffins to cool completely, then enjoy your flavors of fall.
    Gluten free apple muffins served on a white dessert plate; set next to the cooling rack of more muffins.

Nutrition Information Per Serving

Calories: 189kcal | Carbohydrates: 27g | Protein: 3g | Fat: 9g | Saturated Fat: 5g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.3g | Cholesterol: 48mg | Sodium: 118mg | Potassium: 69mg | Fiber: 2g | Sugar: 15g | Vitamin A: 286IU | Vitamin C: 1mg | Calcium: 35mg | Iron: 1mg

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