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Gluten Free Apple Butter Muffins

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Here is your answer for an easy-to-follow recipe for small batch gluten free apple muffins – with double the apple and a crunchy-sweet streusel topping.  The combination of tasty gluten free flours, aromatic spices, fresh apples, and apple butter, make these muffins so flavorful that they rival any traditional muffin!

Delicious inside of an apple gluten free muffin dotted with apple chunks.

Rise And Shine To apple Muffins

The days may be shorter and the air may be crisp, but one delicious constant remains:  the irresistible call of fresh apples.  And what better way to celebrate all things apple than with a warm, fluffy muffin in hand, promising a double burst of apple flavor and fragrant spices in every bite?

Though these apple butter muffins may be gluten free, they are certain to be devoured by the gluten free and traditional muffin enthusiasts.   Tasty oat flour serves as the base of these incredibly moist muffins – so good, that you won’t be able to tell the muffins are free of gluten!

Two apple streusel gluten free muffins stacked and one with the cupcake liner peeled back.

Why I Love These gluten free muffins

Store-bought muffins move over.  There is a new muffin that I can make at home that is just as good and features all of the qualities you love about a bakery-style muffins.

  • Cloud-like Fluffiness – Ditch the frustration of dense, crumbly gluten-free muffins. Along with my gluten free pumpkin muffins and gluten free chocolate chip muffins, this recipe utilizes a magical blend of flours that yield tender, melt-in-your-mouth muffins that rival their gluten-full counterparts. 
  • Apple Burst Symphony – Forget subtle hints of fruit – these muffins are a celebration of apples! Juicy diced apples and smooth apple butter weave a luscious melody in every bite, their tartness perfectly balanced by the warm embrace of cinnamon. 
  • Buttery Kiss of Sweetness: The crunch of the streusel atop each muffin elevates the experience to a whole new level. This delightful burst of buttery sweetness adds texture that keeps your taste buds singing. 
  • Warm & Cozy Comfort – These muffins are more than just food – they’re an aromatic hug on a crisp morning. The intoxicating fragrance of cozy spices wafts through your kitchen, instantly creating a sense of warmth and comfort. 
  • Dietary-Inclusive – You don’t have to be gluten free to love these muffins. This recipe proves that with thoughtful testing and tasting diligence, alternative flours can create culinary masterpieces.
Delicious streusel topping on a fresh baked breakfast treat set on a wire cooling rack.

Key Ingredients To Make gluten free Apple Muffins

  • Fresh Apple – Select a firm apple for the best texture and result.  I like to use Honeycrisp apples in these muffins, and my apple pumpkin muffins.  They retain texture when baked and have a tart + sweet flavor.
  • Apple Butter – Apple butter does double duty in these muffins:  it provides an abundance of flavor and contributes to the moistness-factor.
  • Oat Flour – Oat flour provides the structure and protein for these muffins.  It contributes to the soft crumb and lofty rise.
  • Sweet Rice Flour – Sweet rice flour has properties that mimic gluten.  Which, in this recipe will help as a binder and combine with the other flours to achieve the bakery-style muffin.
  • Tapioca Flour – A little tapioca flour will contribute to the soft chew of the muffins.
  • Sugar – A combination of granulated (organic cane sugar in my case!) and light brown sugar provide different dimensions of sweetness.
  • Oil – Coconut oil serves as the fat in these muffins and will keep them super moist.
  • Egg – The egg will impart texture and structure.
  • Spices – The variety of fragrant spices will harmonize with the apples to truly make the flavor sing in these muffins!
A bowl of creamy apple butter on a black plate.

Apple butter imparts even more apple flavor – and moisture – into these breakfast muffins.  The apple-forward flavor is sweet, a little spicy, and deliciously buttery!

Apple cubes in a bowl next to jar of cinnamon.

Fresh Honeycrisp apple chunks add busts of sweetness and crunch to the apple butter muffins!  Combined with aromatic spices for a cozy breakfast treat, perfect for chilly mornings.


Can I use a 1:1 gluten free flour blend?

I recommend sticking with the recipe blend provided. Through testing, I find that the 1:1 gluten free blends to be much drier – which would require adjustments to other ingredients and ratios.

What are some of the best apples to use for baking?

I like to use firm apples so they retain texture and flavor when baked. Honeycrisp, Pink Lady, Braeburn, and Granny Smith are good options.

Do I have to use a muffin liner, or can I bake the muffins without?

You can bake the muffins without the liner. I recommend greasing the muffin cups well to ensure they don’t stick. Keep in mind with the streusel, the butter and sugar may melt down the sides and cause the muffins to stick. Use a sharp knife or offset spatula to help release the muffins.

Can I make these into mini muffins?

Yes! Use a mini muffin pan with optional mini muffin liners. The recipe should yield 10 to 12 mini apple muffins. You will want to start checking the muffins around 10 minutes to see if they are done.

How long will the muffins last?

The muffins will stay moist covered at room temperature for up to 3 days. Beyond that, and they may start to dry out and get crumbly.

Can I freeze the muffins?

Yes! Wrap each muffin tightly in plastic wrap, then place them in a freezer bag for up to 3 months. Thaw at room temperature.

Single gluten free apple muffin on a cute mini cupcake stand.
Delicious inside of an apple gluten free muffin dotted with apple chunks.
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5 from 1 review

Gluten Free Apple Butter Muffins

Yield: 4 Muffins
Here is your answer for an easy-to-follow recipe for small batch gluten free apple muffins – with double the apple and a crunchy-sweet streusel topping.  The combination of tasty gluten free flours, aromatic spices, fresh apples, and apple butter, make these muffins so flavorful that they rival any traditional muffin!
Prep20 minutes
Cook22 minutes
Total42 minutes



Streusel Topping

Gluten Free Apple Butter Muffins


  • Preheat the oven to 350F degrees and adjust the oven rack to the middle position. Line a muffin pan with 4 muffin liners.

Streusel Topping

  • In a small mixing bowl, whisk together the oat flour, tapioca flour, sugar, and salt. Add the butter cubes and using your finger or two forks, cut the butter into the dry ingredients until moistened and crumbly. Refrigerate until ready to use.
    3 tablespoons gluten free oat flour, 1 tablespoon tapioca flour, 1 tablespoon organic cane sugar, ⅛ teaspoon salt, 1 tablespoon unsalted butter, cold and cut into cubes

Gluten Free Apple Butter Muffins

  • In a small mixing bowl, whisk together the oat flour, sweet rice flour, tapioca flour, baking powder, salt, and spices.
    6 tablespoon gluten free oat flour, ¼ cup sweet rice flour, 2 tablespoons tapioca flour, ½ teaspoon baking powder, ¼ teaspoon salt, ¼ teaspoon ground allspice, ¼ teaspoon ground cardamom, ¼ teaspoon ground ginger, ¼ teaspoon ground cinnamon
  • In a medium mixing bowl, add the oil and sugars. Stir to combine. Add the egg and stir to fully incorporate. Add the apple butter and mix until combined and smooth.
    2 tablespoon cold pressed refined coconut oil, melted, 3 tablespoons light brown sugar, 3 tablespoons organic cane sugar, 1 large egg, room temperature, 3 tablespoons apple butter, room temperature
  • Sprinkle the dry ingredients over the wet and stir until no dry streaks remain. Add the chopped apples and mix until just combined. Let the batter rest for at least 5 minutes to allow the flours to hydrate and flavor develop. Note – It is your choice to either peel the apple, or leave the skin on. I leave the skin on for extra texture.
    ¼ cup apples, chopped
  • Spoon the batter equally into the prepared muffin cups. Sprinkle the tops with equal amounts of the streusel.
  • Bake the muffins for 22 minutes or until they are springy to the touch and a toothpick inserted in the middle comes out mostly clean.
  • Cool the muffins in the pan set on a wire cooling rack for 10 minutes. Then transfer to the wire rack to cool completely. Note – I find gluten free baked goods taste better when they have had a chance to cool completely.
  • Store leftovers covered at room temperature for up to 3 days. Beyond that, the muffins may start to dry out. Well wrapped muffins can also be frozen for up to 3 months and thaw at room temperature.
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  • Serving Size – I have only tested this recipe as a small batch.  I can’t say for certain how doubling the ingredients will turn out.  If you try it, let me know!
  • Best Apples For Baking – I like to use Honeycrisp apples for their firm texture and sweetness.  Any firm apple will work – like Granny Smith, Pink Lady, or Braeburn.
  • To Peel, Or Not Peel – This is your choice.  I do  not peel the apple because I like the texture.  
  • Apple Butter – Any apple butter will work.  
  • Brown Sugar – I recommend light brown sugar because dark may add too much moisture to the muffins and make them too dense.
  • Substitutions – The recipe has only been tested with the ingredients listed.  You could try to swap a Paleo flour blend 1:1.  However, I don’t recommend an all purpose gluten free 1:1 blend as I find it to be much drier.  
  • Storing and Freezing – Store the muffins covered at room temperature for up to 3 days.  They can also be wrapped tightly in plastic wrap and placed in a freezer bag, and frozen for up to 3 months.  Thaw at room temperature.
Course: Breakfast
Cuisine: American
Author: Erin Cernich


Calories: 336kcal | Carbohydrates: 52g | Protein: 5g | Fat: 13g | Saturated Fat: 8g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.1g | Cholesterol: 54mg | Sodium: 297mg | Potassium: 130mg | Fiber: 2g | Sugar: 26g | Vitamin A: 163IU | Vitamin C: 1mg | Calcium: 62mg | Iron: 1mg
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch gluten free and traditional desserts - all homemade, all simple, and all for you! Click here to learn more about me!

5 from 1 vote (1 rating without comment)

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