Gluten-Free Cinnamon Apple Muffins Recipe

By Laura Fuentes Updated Jan 2, 2025

4.95 from 35 votes

Recipe

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Make these gluten-free apple muffins for breakfast, or keep a stash in your freezer for your next cup of coffee.

You’ll also achieve the best muffin texture, learn which gluten-free flour to use, plus all the make-ahead and storage tips!

basket of apple fritter muffins with butter

Best-Ever Gluten-Free Cinnamon Apple Muffins

These gluten-free cinnamon apple muffins have a crumbly texture. It’s a simple recipe you can make in half an hour from start to finish with an all-purpose gluten-free flour!

Each bite of these gluten-free muffins has tender, juicy apple pieces with hints of cinnamon that your tastebuds will love. Whether you make them for the weekend or keep a stash in the freezer, they’re perfect to enjoy with a cup of coffee at home or on the go.

You can also prep the batter the night before and in the morning, take them out of the fridge while the oven preheats, and in just 20-ish minutes, you’ll transform your entire house with the cinnamon scent of baked goods!

Ingredients

With those basic pantry staples you always have on hand, you can bake gluten-free apple muffins as moist and fluffy as the classics. Here’s what you need:

Brown sugar: combined with the cinnamon, creates a delicious crust.
Ground cinnamon: a classic apple companion!
Apple: any variety, peeled and chopped in small even sized pieces.
Sugar: a basic staple for muffin’s batter.
Butter: softened, not melted, to add a delicious buttery flavor. You can swap it for coconut oil to make the muffins dairy-free.
Eggs: help bind the ingredients.
Vanilla extract: makes everything taste even better!
Gluten-free flour: all-purpose gluten-free baking flour mix that includes xantham gum. Below, I share more details about the flour mixes and brands I’ve tested. Need a different option? You can make my Gluten-Free Cranberry Orange Muffin recipe with oat flour!
Baking powder: rise the batter and give these muffins a fluffy texture.
Milk: the liquid we need for this recipe. You can use coconut milk instead for dairy-free muffins.

three side by side images of apple fritter muffin ingredients

How to Make Gluten-Free Apple Muffins

Once you see how easy these gluten-free apple muffins are to make, you’ll make this recipe often. It’s all about combining ingredients in the right order and popping them into the oven!

Check the step-by-step:

Prep the oven
Preheat oven to 350 degrees F (175 degrees C) and line a muffin pan with 12 paper liners.
Prep the cinnamon mix
In a small bowl, combine the brown sugar and cinnamon.
Make the batter
In a large bowl or the bowl of your stand mixer, beat the sugar and butter until smooth and creamy. Add in eggs, 1 at a time, and mix until incorporated; add vanilla extract.
Sift and combine
Sift the flour and baking powder together in a bowl and add to the wet ingredients. Add in the milk and mix until the batter is smooth.
Fill the muffin pan
Pour about 2 tablespoons of batter into each muffin cup (halfway full) then distribute the apple pieces between the muffin cup. Top with additional batter, about another 2 tablespoons, covering the apples.
Top with cinnamon
Sprinkle each muffin with ½ to 1 teaspoon of the brown sugar mixture. Using the back of a fork, gently swirl brown sugar and cinnamon mixture into the muffin batter.
Bake to perfection
Place the muffins in the preheated oven to bake for 22 minutes or until golden brown and a toothpick inserted in the center comes out clean.
Cool down and enjoy!
Remove from oven and allow to cool for 10 minutes before removing from the pan and serving.

Watch this video to see these Gluten-Free Apple Muffins come together:

Need the classic Apple Muffin recipe? Check this post.

Success Tips for Gluten-Free Muffins

The key to successful gluten-free baked goods is the flour, both in how you measure the flour and the type you use. Here are my recommendations for great muffins:

Measure correctly:
Use a spoon to fill your measuring cup so your flour is not packed into the cup. Sweep the top to remove any excess and dump it into the bowl.

Include xanthan gum:
Make sure the gluten-free all-purpose flour you use includes xanthan gum. This binds the types of flours used and adds texture.

1:1 All-Purpose Flour mixes:
My go-to 1:1 flour mis is Bob’s Red Mill Gluten-Free 1 to1 Baking Flour. I’ve made this recipe with King Arthur Flour Measure for Measure, Cup4Cup (blue bag), Pamela’s Gluten Free Pancake & Baking Mix, Namaste Gluten-Free Perfect Flour Blend.

Homemade mixes:
If you make your own gluten-free flour mix, please use one that contains enough starch % to yield a good texture in crumbly baked goods, like quick breads and pancakes and that includes ½ teaspoon of xantham gum for the amount of flour listed in the recipe below.

How to Freeze & Thaw These Muffins

Once the muffins have cooled down, place them on a baking sheet and freeze them for about one hour. Once frozen, transfer the muffins to a freezer-safe zip bag and store them in the freezer for up to 3 months. This method is super convenient to have muffins ready to eat on busy mornings.

You can also freeze the muffin batter in paper liners as shown in this post and bake them frozen.

Thaw the muffins on the counter, overnight in the fridge, or microwave them for about 30 seconds to one minute each, and they’re ready to be enjoyed.

baked apple fritter muffin for breakfast inside a lunchbox with plain yogurt

Other Gluten-Free Breakfast Options

When following a gluten-free diet, you can still enjoy delicious breakfasts, such as these epic GF Blueberry Pancakes and these Banana Almond Flour Pancakes. For incredible morning meals to eat on the go, you need to try these Healthy Oatmeal Breakfast Cookies.

Gluten-Free Apple Muffins

Servings: 12 muffins

Prep Time: 20

Cook Time: 22

Total Time: 42

Make these gluten-free apple muffins for breakfast, or keep a stash in your freezer for your next cup of coffee.

4.95 from 35 votes

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Ingredients

For the muffins:

1 apple, any variety, peeled and chopped in small even sized pieces
½ cup sugar
½ cup butter, softened at room temperature (not melted)
2 large eggs
1 ½ teaspoons vanilla extract
1 ⅓ cups all-purpose gluten free baking flour mix*
1 ¾ teaspoons baking powder
½ cup milk

Cinnamon Sugar Topping:

⅓ cup brown sugar
1 teaspoon ground cinnamon

Instructions

Prep:

Preheat oven to 350 degrees and line a muffin pan with 12 paper liners.
In a small bowl, combine the brown sugar and cinnamon, set aside.

For the Muffins:

In a large bowl or the bowl of your stand mixer, beat the sugar and butter until smooth and creamy. Add in eggs, 1 at a time, and mix until incorporated; add vanilla extract.
In another bowl, sift the flour and baking powder together.
Add the flour mixture slowly to the butter-sugar bowl and combine. Add in the milk and mix until the batter is smooth.
Fill each muffin cup with about 2 tablespoons of batter (halfway full) then distribute the apple pieces between the muffin cup. Top with additional batter, about another 1-2 tablespoons, covering the apples.
Top each muffin with ½ to 1 teaspoon of the brown sugar mixture. Using the back of a fork, gently swirl brown sugar and cinnamon mixture into the muffin batter.
Bake the muffins in the preheated oven for 22 minutes or until golden brown and a toothpick inserted in the center comes out clean.
Remove from oven and allow to cool for 10 minutes before removing from the pan and serving.

Notes

The type of flour mix you use will make a big difference. I have tried this recipe with King Arthur Flour All Purpose Gluten-Free Flour, King Arthur Flour All Purpose Gluten Free Baking Flour, Cup4Cup (blue bag), Pamela’s Gluten Free Baking Mix (orange bag), Pamela’s All-Purpose Gluten Free Flour Mix (blueish/purple bag), Namaste Gluten-Free Perfect Flour Blend.
Please note that if you make your own mix you must make sure you add xanthan gum to help bind your flour starches together (the mixes above already have it). I can’t advise on other blends since I haven’t tried it. If you use another mix successfully, please leave a comment for others to read.