Looking to make gluten-free muffins? This gluten-free muffin recipe can produce all sorts of muffin varieties and flavors. It’s a tried-and-true recipe that creates soft, bakery-style muffins every time!

Yogurt and mixing the batter in a special way are the secret tricks to the BEST gluten-free muffins you’ll ever make! Check out this blog post for all the tips.



 

If you’re looking for a reliable base gluten-free muffin recipe to add all your favorite mix-ins, you’re in the right place. I’ve tried many gluten-free muffin recipes over the years. After a lot of trial and error, this is the recipe I keep coming back too!

For more gluten-free muffin recipes, check out these gluten-free pumpkin muffins, gluten-free banana muffins and gluten-free blueberry muffins.

Table of Contents

Why this gluten-free muffin recipe is amazing!

These muffins stand out from the rest:

Easy to prepare
Light and fluffy crumb
 (from using coconut oil and not butter)
Moist and flavorful (from whole milk yogurt)
Not dense or crumbly (a high quality gluten-free flour prevents these muffins from being crumbly)
Soft and cakey
Tall muffin tops
 (from a high oven temperature during the first 10 minutes of baking

VIDEO: How to Make Gluten-Free Muffins!

Ingredients for the Gluten-Free Muffin Batter

These gluten-free muffins are made with simple ingredients and 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!

overhead shot of ingredients to make gluten free muffins
  • Gluten-Free 1:1 Baking Flour: These gluten-free muffins turn out best when you use a high-quality gluten-free flour blend. Look for flour blends that contains xanthan gum so the muffins have the structure they need. This is my favorite brand.
  • Whole Milk Plain Yogurt: Full-fat (not greek) plain yogurt is the key to the best 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 melted butter, I find that vegetable or coconut oil makes for a fluffier texture in gluten-free cakes and muffins.
  • Lemon Juice: Lemon juice not only adds a nice zing to the muffins and brings out the blueberry flavor, it also reacts with the baking soda and baking powder to help to tenderize the the crumb.
  • Mix-Ins: There are endless mix-in options for these muffins!

Dairy-Free? You can easily swap in dairy-free yogurt for the whole milk yogurt. My favorite brand is Kite Hill plain almond milk yogurt. Unfortunately this recipe will not work with flax eggs.

overhead shot of ingredients to mix-in to gluten-free muffins

Endless mix-in options

Here are some ideas for mix-ins. See below for more specific favorite combinations!

  • Fruit: fresh blueberries, frozen berries, Apples, pears (It’s best to shred apple and finely dice pears. Big chunks may negatively effect the texture.)
  • Chocolate: Any kind!
  • Nuts
  • Lemon zest
  • Poppyseeds
  • Extracts for more flavor such as almond, lemon or vanilla extract

Note: Just make sure you don’t add too much of anything. Gluten-free muffins have a more delicate structure so it’s important not to add more than 1 cup of mix-ins.

muffin or glaze topping

Topping Options

When it comes to gluten-free muffin toppings you have 3 different options.

  1. A simple sprinkle of raw sugar
  2. Lemon glaze (1 cup powdered sugar + 2-3 tablespoons lemon juice)
  3. Crumb topping (recipe in these gluten-free orange cranberry muffins)

How to Make Gluten-Free Muffins from Scratch

how to mix together the muffin batter in the stand mixer
  • Preheat the oven to 425F. Line a standard muffin pan with muffin cups or 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 (or a large bowl with an electric mixer), add the eggs (room temperature is best!) and sugar. Beat together until the mixture is light and fluffy, about 5 minutes.
  • With the mixer running on low, slowly drizzle in the melted coconut oil. (Do this slowly so you keep the air you mixed into the eggs/sugar.) Add the lemon juice and mix.
mixing dry ingredients and yogurt into batter
  • With the mixer running on low, add ⅓ of the flour mixture followed by ½ of the yogurt to the wet ingredients. 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.
raspberry and white chocolate mixing into batter
  • Fold in your mix-ins of choice with a rubber spatula. Using cookie scoop or large spoon, portion batter evenly into the prepared muffin tins.  Sprinkle the raw sugar evenly over the top of the muffins.
  • 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!
side by side picture of blueberry and white chocolate raspberry muffin

Favorite Combinations

Once you have an amazing base muffin recipe, the variations you can make are endless.

Here are a few of my favorite combinations:

  • White chocolate raspberry (1/2 cup raspberries + 1/2 cup white chocolate chips + raw sugar for topping)
  • Chocolate chip streusel (1 cup chocolate chips + crumb topping)
  • Triple berry glazed (1 cup of mixed berries + lemon glaze topping)
  • Lemon poppyseed (2 tablespoons poppyseeds + lemon glaze)
  • Apple cinnamon (1 cup shredded apples + crumb topping)

For another master gluten-free recipe check out this post on how to make gluten-free scones!

side by side picture of gluten free triple berry and gluten free chocolate chip muffins

Gluten-Free Muffin FAQ

Which gluten free flour is best for muffins?

It is best to use a high-quality 1:1 or measure-for-measure baking flour in gluten-free muffins. Look for a brand that contains xanthan gum as a binder.

How do you make gluten free muffins more moist?

The addition of yogurt or sour cream helps make gluten-free muffins more moist. Plain dairy-free yogurt will also work.

How long do gluten free muffins last?

Gluten-Free muffins are best eaten the day they are made. This is especially true if the muffins contain fruit or has a glaze topping. Gluten-free muffins can soak up too much moisture from fruit after a day or so. Muffins made with just nuts, chocolate chips or poppy seeds can last up to 2 days stored in an airtight container.

Can I freeze gluten free muffins?

Yes! Gluten-free 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. 

overhead shot of gluten-free muffins on white plate

More Gluten-Free Recipes

Happy gluten-free baking! I hope this guide helps you make delicious gluten-free muffins. If you make this recipe, please leave me a comment/rating below! I’d love to hear what combinations you try!

5 from 35 votes

Gluten-Free Muffins (Endless Mix-ins!)

Prep Time 20 minutes
Cook Time 20 minutes
Total Time 40 minutes
Servings 12 muffins
Looking to make gluten-free muffins? This gluten-free muffin recipe can produce all sorts of muffin varieties and flavors. It's a tried-and-true recipe that creates soft, bakery-style muffins every time!
Yogurt and mixing the batter in a special way are the secret tricks to the BEST gluten-free muffins you'll ever make! Be sure to watch the video below too!

Video

Ingredients

Dry Ingredients:

  • 1 ½ cups gluten-free 1:1 baking flour
  • ½ cup almond flour (or 1/3 cup more gluten-free 1:1 baking flour)
  • 1 ½ teaspoons baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon kosher salt
  • ¼ teaspoon nutmeg

Other:

  • 2 large eggs
  • cup sugar
  • ½ cup vegetable oil or melted coconut oil
  • 1 tablespoon lemon juice
  • 1 cup whole-milk yogurt
  • 1 cup mix-ins of choice (see ideas below)
  • 2 tablespoons raw sugar optional

Instructions 

  • 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 sugar. Beat together until the mixture is light and fluffy, about 5 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.) Add the lemon juice and mix.
  • 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 blueberries with a rubber spatula. Using kitchen scoop or large spoon, portion batter evenly into prepared muffin tin. Sprinkle the raw sugar evenly over the top of the muffins.
  • 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

Nut-Free? Use another 1/3 cup gluten-free 1:1 baking flour in place of the almond flour. 
Dairy-Free? You can easily swap in dairy-free yogurt for the whole milk yogurt. My favorite brand is Kite Hill plain almond milk yogurt.
Favorite Combinations: Be sure to only add up to 1 cup of mix-ins. 
  • White chocolate raspberry (1/2 cup raspberries + 1/2 cup white chocolate chips + raw sugar for topping)
  • Chocolate chip streusel (1 cup chocolate chips + crumb topping)
  • Triple berry glazed (1 cup of mixed berries + lemon glaze topping)
  • Lemon poppyseed (2 tablespoons poppyseeds + lemon glaze)
  • Apple cinnamon (1 cup shredded apples + crumb topping)
 
Topping Options:
  1. A simple sprinkle of raw sugar
  2. Lemon glaze (1 cup powdered sugar + 2-3 tablespoons lemon juice)
  3. Crumb topping (recipe in these gluten-free orange cranberry muffins)
 
Ingredient Notes
  • Gluten-Free 1:1 Baking Flour: These 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 (not greek) plain yogurt 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.
  • Melted Coconut Oil: These muffins call for coconut oil instead of butter. As much as I love butter, I find that coconut oil makes for a fluffier texture in gluten-free cakes and muffins.
 
Storage/Freezing
  • To Store: These muffins are best served the day they are made. They can be stored in a ziploc-bag at room temperature for up to 1 day.
  • To Freeze: They can also be frozen by wrapping each muffin individually in plastic wrap then storing in a ziploc-bag. To reheat from frozen, remove the plastic and microwave the muffin for 20 to 30 seconds, until thawed. 

Nutrition

Calories: 247kcal | Carbohydrates: 27g | Protein: 5g | Fat: 14g | Saturated Fat: 9g | Trans Fat: 1g | Cholesterol: 30mg | Sodium: 166mg | Potassium: 160mg | Fiber: 2g | Sugar: 16g | Vitamin A: 67IU | Vitamin C: 2mg | Calcium: 70mg | 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. 5 stars
    Delicious and everyone I shared with did not know they were GF. I ‘accidentally’ used flavoured yoghurt (vanilla…still high fat and still GF) and it was a happy accident….even more delicious than when I made with plain. Think I might make them this way from now on. Thanks for this recipe…best one ever (with plain yoghurt).

    1. That’s great to know they turned out delicious with plain vanilla yogurt! I’ll have to try that myself sometime!

  2. 5 stars
    These muffins are awesome and I make them all the time! Now that it’s fall, how can I make a cozy fall pumpkin version of these? If I add pumpkin purée would I reduce the oil? Or maybe reduce the yogurt? Or just add the pumpkin as an add in? I was thinking maybe a pumpkin pecan muffin? Or maybe pumpkin apple? Or cranberry pumpkin? Not sure… so many possibilities!

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