Gluten Free Apple Cinnamon Muffins
These gluten-free apple cinnamon muffins are soft, moist, and filled with fresh apple pieces, cinnamon, and nutmeg. They come together in one bowl and are ready in about 35 minutes, so they’re easy enough for breakfast, snacks, or a make-ahead batch.

John made these for me when I followed a gluten-free diet for a while, and they quickly became one of my favorite muffin recipes. The texture is tender, not dry or crumbly, and you really wouldn’t guess they’re gluten-free.
Kim’s Tips for the Best Gluten Free Apple Cinnamon Muffins
The flour blend you use matters in this recipe. Use a gluten-free 1-to-1 baking flour that already contains xanthan gum. We’ve used blends like King Arthur Measure for Measure and Bob’s Red Mill 1-to-1 Baking Flour. Plain gluten-free all-purpose flour without a binder won’t work the same way.
You can replace the melted butter with the same amount of neutral oil, such as vegetable or canola oil. The muffins will still be moist, but they won’t have quite as much buttery flavor.
Don’t miss my other apple recipes, including easy apple crisp, apple butter hand pies, and Granny Smith apple pie.
How to Make Gluten Free Apple Cinnamon Muffins
Prepare the pan and apples: Preheat the oven to 375°F, and line a 12-cup muffin pan with paper liners. Peel, core, and dice the apples into small, evenly sized pieces.

Mix the batter: Add the gluten-free flour blend, milk, sugar, melted butter, eggs, baking powder, vanilla, salt, cinnamon, nutmeg, and baking soda to a large mixing bowl. Stir just until the ingredients are combined. The batter will be fairly thick and may have a few small lumps.

Fold in the apples: Set aside about ¼ cup of the diced apples for the tops. Gently fold the remaining apples into the batter.

Fill the muffin pan: Use a ⅓-cup measuring cup to divide the batter between the muffin cups, filling each one about halfway to two-thirds full. Dot the reserved apple pieces over the tops.

Bake: Bake for 20 to 25 minutes, until the tops are golden brown and a toothpick inserted into the center comes out clean.
Let the muffins cool in the pan for a few minutes, then move them to a wire rack. They’re especially good served warm while the apple pieces are still soft.
Pack the muffins with homemade apple chips for an easy apple-themed snack.

Ingredients
- 1 ¾ cups gluten-free 1-to-1 baking flour blend
- 1 cup whole milk
- ¾ cup granulated sugar
- ½ cup unsalted butter, melted and cooled slightly
- 2 large eggs
- 2 teaspoons baking powder
- 1 teaspoon vanilla extract
- ½ teaspoon salt
- ½ teaspoon ground cinnamon
- ¼ teaspoon ground nutmeg
- ¼ teaspoon baking soda
- 2 medium apples, peeled, cored, and diced
💌 Don't forget to save this recipe!
Instructions
- Preheat the oven to 375°F, and line a 12-cup muffin pan with paper liners.
- Add the gluten-free flour blend, milk, sugar, melted butter, eggs, baking powder, vanilla, salt, cinnamon, nutmeg, and baking soda to a large mixing bowl. Stir just until combined. Do not overmix.1 ¾ cups gluten-free 1-to-1 baking flour blend1 cup whole milk¾ cup granulated sugar½ cup unsalted butter2 large eggs2 teaspoons baking powder1 teaspoon vanilla extract½ teaspoon salt½ teaspoon ground cinnamon¼ teaspoon ground nutmeg¼ teaspoon baking soda
- Fold in the diced apples, reserving about ¼ cup for the tops of the muffins.2 medium apples
- Use a ⅓-cup measuring cup to divide the batter between the muffin cups, filling each one about halfway to two-thirds full. Place the reserved apple pieces over the tops.
- Bake for 20 to 25 minutes, until the tops are golden brown and a toothpick inserted into the center comes out clean.
- Let the muffins cool in the pan for a few minutes, then transfer them to a wire rack. Serve warm or cool completely before storing.
Notes
- Use a gluten-free 1-to-1 baking flour blend that contains xanthan gum. We used King Arthur Measure for Measure. Bob’s Red Mill Gluten Free 1-to-1 Baking Flour is a similar option.
- Apple pie spice may be used in place of the cinnamon and nutmeg.
- Store the muffins in a single layer in an airtight container lined with a paper towel. Keep them at room temperature for up to 3 days or refrigerate them for 4 to 5 days.
- To freeze, wrap the muffins individually and place them in a freezer-safe container for up to 2 months. Thaw at room temperature or warm an individual muffin in the microwave for 10 to 15 seconds.


Excellent gluten free recipe. I used raw sugar & apple pie spice in place of cinnamon & nutmeg & sprinkled cinnamon & sugar on top. Delicious!
Thank you Jill! Kim and I are glad you liked the recipe. Thank you again for coming back to comment on the recipe. Have a lovely day 🙂
Hi ,
I made these today – I’d post a photo but I don’t think I can ? Only change I made was adding cinnamon sugar to unbaked muffin tops & then drizzled cooled muffins with a cinnamon sugar glaze .
Thank you, Cathy! That’s sounds like a great modification. Kim and I are thrilled you enjoyed the muffins. Thank you again for coming back to comment on and rate the recipe card. Have a lovely day 🙂
Hi ,
I made these today – I’d post a photo but I don’t think I can ? Only change I made was adding cinnamon sugar to unbaked muffin tops & then drizzled cooled muffins with a cinnamon sugar glaze .
Yum! I bet these muffins taste similar to an apple pie. I haven’t made breakfast muffins in a very long time.
This looks like a delicious recipe. I have rebooking for a new gluten free muffin to add to the ones I have been making. I love the Apple and cinnamon combo
Those look great. I like the big chunks of apples still in tact – they add texture, too, I’m sure, in addition to a taste explosion.
Appreciate your in-depth easy to follow instructions for this recipe. Great pictures too! This recipe sure looks good!
I love apple recipes. These muffins look so yummy. I cannot wait to try out this recipe for myself.
Yummy!! Cinnamon Apple Muffins are a favorite of mine. I love how you reserved some apple for the tops of the muffins!