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    Home » Recipes » Gluten Free Dessert Recipes

    Gluten Free Apple Muffins with Applesauce

    Last Modified: Sep 20, 2025 by Chelsea Joy · This post may contain affiliate links · This blog generates income via ads

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    Warm spices and fresh apples make these gluten free apple muffins the perfect fall treat!

    Fluffy and made bakery-style for added lift, these muffins are wonderfully moist without being mushy.

    Overhead view of a batch of gluten free apple muffins lined up on a wire rack

    Why we love these muffins

    TASTE OF FALL: While I'm all about high protein meals, sometimes we just crave a treat. In early fall when apples just come into season, these muffins hit the spot!

    TENDER & FLUFFY: These muffins are gluten free, but you wouldn't know it - they're plenty tender and fluffy!

    BAKERY STYLE: I'll give you all my top tips for big, fluffy, bakery-style muffins. The secret is lots of leavening!

    Jump to:
    • Why we love these muffins
    • Ingredients of note
    • Tips for fluffy bakery-style gluten free muffins
    • Instructions
    • Common substitutions
    • FAQs
    • More gluten free apple baked goods
    • 📖 Recipe
    Ingredients for gluten free apple muffins with applesauce, with text labels for each ingredient

    Ingredients of note

    APPLES: My favorite apples for baking are Braeburn and Granny Smith. Either will work well here! For best results, you'll peel and core the apples

    GLUTEN FREE FLOUR: My go-to blend is Bob's Red Mill 1:1 Baking Flour.

    You can find it in almost every grocery store, it works well for a variety of baking, and it already contains xanthan gum (an important ingredient in gluten free baking.) I use it for almost all my baking recipes!

    ALMOND FLOUR: A little almond flour keeps these muffins moist gives them a slightly nutty flavor that invokes the warm cozy flavors of fall.

    APPLESAUCE: I replaced the typical butter and milk in my standard gluten free muffin recipe with applesauce - more apple flavor and works just was well to keep these muffins moist!

    GREEK YOGURT: I still used Greek yogurt in this recipe (you can use sour cream as well), since the slight acidity in Greek yogurt/sour cream helps create the leavening you need for bakery-style muffins!

    SPICES: Cinnamon, cardamom, and nutmeg are my spices of choice to add cozy autumn flavors to these gluten free apple muffins.

    Two apple muffins stacked on top of one another, with more muffins in the background

    Tips for fluffy bakery-style gluten free muffins

    - Batter will be thick

    The batter for these muffins should be just on the edge of "wow, this might be too thick for muffin batter." Trust the process!

    However, if it is SO thick that you can't plop it into the muffin liners, you may need to add an additional tablespoon or two of applesauce to help thin it out.

    - Lots of leavening

    As mentioned in the ingredient notes, gluten free baked goods need a little extra help to create the structure and fluffiness we love.

    So for these gluten free apple muffins, I employed several strategies to get the lift needed.

    Using both baking soda and baking powder, adding apple cider vinegar, and leaning on the acidity in Greek yogurt or sour cream all help in this department.

    - Don't overmix!

    Overmixing the batter leads quickly to tough, not fluffy muffins.

    Mix the batter just until all the ingredients are combined. For this reason, I don't suggest using an electric mixer.

    - Fill the muffin liners to the top

    Want to get those big, beautiful, bakery-style muffin tops? Fill those muffin liners, baby!

    General advice suggests filling ¾ full, but this recipe will ask you to fill them to the top. Avoid overflowing the muffin liners, though, as that will create top-heavy muffins.

    - Only use half the muffin tin

    Because we're filling those muffin liners to the top and we want the domes to lift and spread beyond their boundaries, you'll leave half the tin empty. Skip every other indent to give the domes room to grow without bumping up against each other.

    I almost always end up baking in 2 batches because of this.

    Closeup of a muffin with an oat streusel topping

    Instructions

    1. Peel and chop apples: You'll need about 2 cups of chopped apples for this recipe!
    2. Combine dry ingredients: Add the gluten free flour, sugars, baking powder, baking soda, spices, and salt to a bowl and stir to incorporate. I also like tossing the chopped apples in the dry ingredients before mixing with the wet ingredients!
    3. Combine wet ingredients: In a separate bowl, stir together the applesauce cooled melted butter, Greek yogurt or sour cream, eggs, apple cider vinegar, and vanilla.
    4. Mix it all together: Add the dry ingredients to the wet and stir just until no dry flour remains.
    5. Bake! Add the batter to a lined muffin tin and bake at 425 degrees F for 7 min before dropping to 350 degrees F for 12-15 minutes.
    Overhead closeup of the tops of gluten free apple muffins, some with a streusel topping

    Common substitutions

    Need to change things up? Here are a few common substitutions to make for these gluten free apple muffins!

    To make these muffins nut free

    Simply replace the almond flour with more gluten free flour blend.

    If making the streusel, make the same substitution. At that point, the muffins should be nut free.

    Can I add nuts instead?

    Sure can! Add up to ½ cup chopped toasted walnuts or pecans after mixing the wet and dry ingredients.

    What if I don't use your recommended flour blend?

    You can use whatever gluten free 1:1 flour blend you'd like - King Arthur's should work well, too! Just make sure the blend you use includes xanthan gum. Otherwise, add ½ teaspoon xanthan gum to the flour.

    Unfortunately, I can't test every gluten free flour blend, so I can't speak to the overall texture.

    FAQs

    My muffins didn't rise. What happened?

    Usually expired baking soda or baking powder are to blame for baked goods that don't rise. We often keep these ingredients around in perpetuity without checking whether they still work!

    To test if your baking soda or powder are fresh, put ¼ teaspoon soda or powder in a cup and add a small amount of vinegar or very hot water. If it doesn't bubble, it should be replaced.

    What apples work best for baking?

    I like using Braeburn or Granny Smith apples - they are easy to find and firm enough for baking!
    Other firm-fleshed varieties that hold up well in baking include Jonagold, Honeycrisp, Pink Lady, and SweeTango.

    Can I make these muffins nut free?

    Yes! Simply replace the almond flour with more gluten free flour blend. If making the streusel, make the same substitution. At that point, the muffins should be nut free.

    Overhead view of gluten free apple muffins, one half-eaten on a cutting board

    More gluten free apple baked goods

    Have more apples to use? Try Stovetop Apple Butter or my spouse's favorite Apple Walnut Bundt Cake! For a paleo version of apple muffins, try Apple Pecan Streusel Muffins.

    • Pumpkin Spice & Apple Dutch Baby | DoYouEvenPaleo.net
      Gluten Free Pumpkin Spice & Apple Dutch Baby
    • Paleo Apple Walnut Bundt Cake | DoYouEvenPaleo.net
      Gluten Free Apple Bundt Cake with Walnuts
    • Paleo German Apple Pancake | DoYouEvenPaleo.net
      Gluten Free German Apple Pancake
    • Gluten Free Walnut Apple Crisp Recipe with a scoop of vanilla ice cream with a fork on a wooden board by DoYouEvenPaleo.net
      Gluten Free Walnut Apple Crisp

    Have you made these gluten free apple muffins? I'd love to hear how you enjoyed this treat! Comment below or tag me on Instagram.

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    📖 Recipe

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    Two gluten free apple muffins stacked on top of one another, one with a bite missing, and more muffins behind

    Gluten Free Apple Muffins with Applesauce

    5 Stars 4 Stars 3 Stars 2 Stars 1 Star No reviews
    • Author: Chelsea Joy
    • Prep Time: 15 minutes
    • Cook Time: 23 minutes
    • Total Time: 38 minutes
    • Yield: 12 muffins 1x
    • Category: Dessert
    • Method: Baked
    • Diet: Gluten Free
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    Description

    Warm spices and fresh apples make these gluten free apple muffins the perfect fall treat! Made with lots of leavening for big, bakery-style tops, these muffins have a fluffy, tender texture and great apple flavor.


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    Ingredients

    Units Scale

    For the Muffins:

    • 2 cups + 2 tablespoons Bob's Red Mill gluten free 1:1 flour, spooned and leveled
    • ½ cup almond flour
    • ¼ cup arrowroot flour
    • ⅔ cup cane sugar
    • 2 teaspoons baking powder
    • 1 teaspoon baking soda
    • ¾ teaspoon ground cinnamon
    • ½ teaspoon cardamom
    • ¼ teaspoon ground nutmeg
    • 1 teaspoon fine sea salt
    • ¾ cup applesauce, unsweetened
    • 2 tablespoons butter, melted and cooled
    • ½ cup plain low-fat yogurt or sour cream, room temperature
    • ¼ cup brown sugar, lightly packed
    • 3 large eggs, room temperature
    • 1 teaspoon vanilla extract
    • 1 tablespoons apple cider vinegar
    • 2 cups chopped apples
    • 2-3 tablespoons turbinado or coarse sugar, for topping

    For the Oat Streusel (Optional)

    • ⅓ cup brown sugar
    • 3 tablespoons butter, melted
    • ¼ cup almond flour
    • ⅓ cup rolled oats

    Instructions

    1. Move one oven rack to the middle position and preheat the oven to 425 degrees F.
    2. In a mixing bowl, combine the gluten free flour, almond flour, arrowroot flour, sugar, baking powder, baking soda, cinnamon, cardamom, nutmeg, and sea salt. Stir with a spoon or whisk to fully incorporate ingredients. Add the chopped apples and stir to coat the apples in flour. Set aside.
    3. In a larger mixing bowl, combine the applesauce, melted butter, yogurt/sour cream, brown sugar, eggs, and vanilla extract. Whisk until smooth. 
    4. Gradually mix the dry ingredients into the wet ingredients until a batter is formed - don't overmix, or you'll end up with chewy muffins. 
    5. (Optional) Make the streusel by combining the brown sugar, melted butter, almond flour, and oats in a bowl. Stir until crumbly and combined.
    6. For bakery-style muffins, line a 12-count muffin pan with 6 muffin liners (this leaves room for those extra-big domed tops - meaning you'll have to bake in 2 batches). Fill the liners with about ½ cup of batter, so the batter rests just above the liner. Top the muffins with streusel or turbinado sugar, if desired.
    7. Place one pan in the center of the oven and bake for 7 minutes at 425 degrees F, then (without opening the oven door) decrease the temperature to 350 degrees F and bake for an additional 12-15 minutes or until a toothpick inserted in the center comes out clean. Allow the muffins to cool for a couple minutes before removing to a wire rack. Repeat with the remaining batter, starting with the oven at 425 degrees F. Let the muffins cool completely before eating. Store in an airtight container in the fridge for up to 1 week.

    Did you make this recipe?

    Leave a comment and rating below or tag @chelseajoyeats on Instagram!

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    Hello! I'm Chelsea, the sole author, recipe developer, and photographer behind Chelsea Joy Eats.

    Life should be full of flavor! I've made it my mission to bring you healthy, often high protein and gluten free recipes while also venturing into indulgent desserts. Want to know more?

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