These are the BEST apple muffins I’ve ever made! My #1 tip for gluten-free apple muffins – use a mixture yogurt/oil for the right texture!

These muffins are light and fluffy with tall muffin tops. The sweet apple chunks and slightly crunchy crumb topping take these muffins to the next level. Check out this blog post for all my best tips on baking delicious gluten-free muffins!

Apple muffin with a bite taken out of it

Apple muffins are a crowd favorite, and it’s easy to see why. The combination of cinnamon, ginger, nutmeg, fresh apples, and crumb topping make for one tasty snack. Plus, these healthy apple muffins make a great quick breakfast on the go.

This is a great recipe to make during apple season or any time of year. If you go apple picking with your family, you might be wondering what to do with all of those apples. Well, here you go!

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Whether you use Pink Lady, Honeycrisp apples, Gala apples, or any other combination of apples, you’ll love this gluten-free apple muffin recipe. And you’ll probably have plenty of leftover muffins for a perfect fall breakfast. (Or spring, summer, or winter breakfast!)

Feeling like pumpkin? Try these gluten-free pumpkin muffins.

If you love apples, you also might like these recipes for gluten-free apple crumblegluten-free apple piegluten-free apple cakeapple compote and gluten-free apple crisp!

For more gluten-free muffins try these gluten-free chocolate chip muffins, gluten-free banana muffins and gluten-free blueberry muffins.

Why You’ll Love These Gluten-Free Apple Muffins

  • Easy to prepare
  • Always light and fluffy
  • Moist and flavorful (thanks to whole milk yogurt)
  • Tall muffin tops (bake at a higher temperature for the first 10 minutes to achieve a tall muffin!)

Ingredients You’ll Need for Gluten-Free Apple Muffins

These gluten-free apple muffins are made with easy-to-find pantry staples. Here are a few notes on some of the key ingredients. If you have any other ingredient or substitution questions, please leave me a comment below!

Ingredients for the Apple Mixture

Apple muffin mixture ingredients on the counter
  • Apples: Use a firm sweet-tart variety of apple for this gluten-free apple muffin recipe. I love the tart flavor of Pink Lady or Granny Smith apples.
  • Lemon Juice: Use fresh lemon juice for the best flavor, or you can substitute store-bought lemon juice if it’s what you have on hand.

Ingredients for the Crumb Topping

Apple muffin crumb ingredients in small bowls on the counter
  • Butter: Melted butter gives the crumb topping a delicious, deep flavor. I recommend using the real stuff!
  • Cinnamon: Cinnamon adds the best fall flavor to this recipe, especially with you add an extra dose on top of the muffin.

Ingredients for the Gluten-Free Apple Muffins Batter

Apple muffin batter ingredients spread on the counter
  • Gluten-Free 1:1 Baking Flour: These gluten-free muffins turn out best when you use a high-quality 1:1 gluten-free baking flour. Look for a blend that contains xanthan gum so the muffins have the structure they need. This is my favorite brand.
  • Whole Milk Plain Yogurt: Full-fat plain yogurt (regular, not Greek) is the key to moist, gluten-free muffins! If you use low-fat yogurt, the muffins may be drier. You can also use dairy-free yogurt, such a plain almond milk yogurt.
  • Oil: These muffins call for oil instead of butter. As much as I love butter, I find that vegetable or coconut oil makes for a fluffier texture in gluten-free cakes and muffins.
  • Lemon Juice: Lemon juice adds a nice zing to the muffins, brings out the apple flavor, and helps create a tender crumb.

How to Make Gluten-Free Apple Muffins

Prepare the Apples

A glass bowl with the apple mixture and a spoon

Mix up the chopped apples and apple mixture ingredients in a small bowl. Soaking the apples in lemon juice and sugar causes the apples to macerate, (release their juices). This makes for extra flavorful muffins! Let the apple mixture sit while you prepare the rest of the batter.

Make the Crumb Topping

A glass bowl with crumb topping ingredients and a spoon

Avoid over-mixing the topping to keep the desired large crumbles. If over-mixed, this topping will turn into a thick paste—which isn’t what you want.

Make the Gluten-Free Apple Muffins Batter

A bowl with dry ingredients and a whisk
  • Preheat the oven to 425F. Line a standard muffin pan with paper baking cups.
  • In a medium or large mixing bowl, whisk together the dry ingredients. Set aside.
A stand mixer mixing up the apple muffin batter ingredients
  • In the large bowl of a stand mixer fitted with a paddle attachment, add the eggs and brown sugar. Beat together until the mixture is light and fluffy, about 3 minutes.
  • With the mixer running on low, slowly drizzle in the oil. (Do this slowly so you keep the air you mixed into the eggs/sugar.) 
  • With the mixer running on low, add ⅓ of the flour mixture followed by ½ of the yogurt. Mix the dry and wet ingredients until combined, then add another ⅓ of the flour mixture.
  • Add the rest of the yogurt and mix until combined. Then add the rest of the flour and mix until incorporated. Scrape down the sides and bottom of the mixer and mix for another 15-20 seconds until the muffin batter is totally smooth.
  • Stir in the apple mixture with a rubber spatula until combined. Using a kitchen scoop or large spoon, portion the batter evenly into the prepared muffin tin.
  • Sprinkle the crumb topping evenly over the top of the muffins. (If you want extra tall muffin tops, you can refrigerate the muffins in the pan for 15 minutes before baking.)
  • Bake the muffins for 10 minutes, then turn down the heat to 375F. Continue to bake for another 10-15 minutes, until the muffins are lightly browned on top and a toothpick inserted into the center comes out clean.
  • Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. Enjoy!

Storage/Freezing Instructions

To store: After the muffins have cooled on the cooling rack, you can store muffins with their muffin cups in an airtight container for up to three days.

To freeze: These gluten-free apple muffins can be stored in an air-tight bag and frozen for up to 2 months. To reheat from frozen, remove the plastic and microwave the muffin for 20 to 30 seconds, until thawed. 

Recipe FAQs

What kind of apples are best for muffins?

Granny Smith apples are great for baking, since they bring a tartness to balance out the sweet muffins. Avoid Fuji or Red Delicious apples, which are softer and mild in flavor.

What makes a muffin light and fluffy?

These gluten-free muffins are made light and fluffy by using coconut oil instead of butter in the muffin batter.

What can I do with lots of apples?

Of course, these gluten-free apple muffins are perfect when you need to use up a lot of apples. You can also make applesauce, apple butter, or caramel apples!

Baked apple muffins on the counter

Expert Tips and Tricks

  • Use a sweet-tart, firm apple such as Granny Smith or Pink Lady.
  • If you want extra tall muffin tops, you can refrigerate the muffins in the pan for 15 minutes before baking.
  • For a dairy-free option, substitute the plain yogurt for dairy-free yogurt (such a plain almond milk yogurt).
  • Don’t over-mix the crumb topping, or it will turn into a paste, rather than a crumble!

More Gluten-Free Muffin/Bread Recipes

I hope enjoy your gluten-free apple muffins! If you make this muffin recipe, please leave me a comment/rating below. I’d love to hear what you think!

close up photo of inside of gluten free apple muffin
5 from 15 votes

Gluten-Free Apple Muffins (BEST EVER!)

Prep Time 10 mins
Cook Time 20 mins
Total Time 30 mins
Servings 16 muffins
Who could pass on warm, perfectly spiced apple muffins? The sweet apple mixture and slightly crunchy crumb topping take these muffins to the next level. Plus, they're always light, fluffy, and moist!

Ingredients

For the Apples:

  • 2 apples cut into pea-sized pieces
  • 2 tablespoons lemon juice
  • 2 tablespoons white sugar
  • 1 teaspoon cinnamon

For the Crumb Topping:

  • ½ cup gluten-free 1:1 baking flour 80 grams
  • 1/3 cup packed light brown sugar 67 grams
  • 1 tablespoon white sugar 15 grams
  • 1 teaspoon ground cinnamon
  • 1/4 cup butter melted 60 grams

For the Dry Ingredients:

  • 1 3/4 cups gluten-free 1:1 baking flour 280 grams
  • 2/3 cup almond flour 85 grams
  • 1 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 3/4 teaspoon salt
  • 1/2 teaspoon ground nutmeg
  • 1/2 teaspoon ground ginger

Other:

  • 2 large eggs
  • 1 cup light brown sugar
  • ½ cup vegetable oil or oil of choice
  • 1 cup whole-milk yogurt

Instructions 

Prepare the Apples:

  • In a medium bowl, combine the apples, lemon juice, white sugar and cinnamon. Stir to combine and let sit while you prepare the muffin batter.

Make the Crumb Topping:

  • Mix the gluten-free flour, brown sugar, granulated sugar, and cinnamon together in a small bowl. Stir in the melted butter, and then gently mix in the flour using a fork. Keep the mixture as large crumbles and do not over-mix. If over-mixed, this will turn into a thick paste. Set topping aside.

Make the Muffins:

  • Preheat the oven to 425F. Line a standard muffin pan with paper baking cups.
  • In a medium bowl, whisk together the dry ingredients. Set aside.
  • In the bowl of a stand mixer fitted with a paddle attachment, add the eggs and brown sugar. Beat together until the mixture is light and fluffy, about 3 minutes.
  • With the mixer running on low, slowly drizzle in the oil. (Do this slowly so you keep the air you mixed into the eggs/sugar.)
  • With the mixer running on low, add ⅓ of the flour mixture followed by ½ of the yogurt. Mix until combined then add another ⅓ of the flour mixture. Add the rest of the yogurt and mix until combined. Then add the rest of the flour and mix until incorporated. Scrape down the sides and bottom of the mixer and mix for another 15-20 seconds until the batter is totally smooth.
  • Stir in the apple mixture with a rubber spatula until combined. Using a kitchen scoop or large spoon, portion the batter evenly into the prepared muffin tin. Sprinkle the crumb topping evenly over the top of the muffins. (If you want extra tall muffin tops you can refrigerate the muffins in the pan for 15 minutes before baking.)
  • Bake the muffins for 10 minutes, then turn down the heat to 375F. Continue to bake for another 10-15 minutes, until the muffins are lightly browned on top and a toothpick inserted into the center comes out clean.
  • Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. Enjoy!

Notes

  • Use a sweet-tart, firm apple such as Granny Smith or Pink Lady.
  • If you want extra tall muffin tops, you can refrigerate the muffins in the pan for 15 minutes before baking.
  • For a dairy-free option, substitute the plain yogurt for dairy-free yogurt (such a plain almond milk yogurt).
  • Don’t over-mix the crumb topping, or it will turn into a paste, rather than a crumble!

Nutrition

Calories: 229kcal | Carbohydrates: 37g | Protein: 5g | Fat: 8g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 30mg | Sodium: 192mg | Potassium: 186mg | Fiber: 2g | Sugar: 24g | Vitamin A: 147IU | Vitamin C: 2mg | Calcium: 77mg | Iron: 1mg

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Hi, I’m Erin!

BS Food Science,

MS Nutrition

I believe you can make amazing, gluten-free food with everyday ingredients that everyone will enjoy. I’m here to share my tried-and-true recipes with you!

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Comments

      1. Great question! I actually recommend using Kite Hill Almond Milk yogurt – or another favorite unsweetened plain dairy-free yogurt. Applesauce won’t create the same results.

  1. 5 stars
    Amazing light, fluffy and delicious muffins. Made as directed. I like to make a few kinds of muffins and freeze them so I can have a snack once in awhile. These were great for that, just 25 seconds in the microwave. I’m going to make these next with blueberries, add in some lemon zest, and cut the lemon juice by half. More like a blueberry buckle muffin. Thank you for sharing your amazing recipes!

  2. 5 stars
    I bake muffins once a week and needed a GF option. These were absolutely perfect! So fluffy and delicious! Thank you!

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