These bakery-style gluten-free chocolate chip muffins are so EASY to make. With tall muffin tops and a soft, fluffy interior you’ll want to bake them over and over!

My #1 tip for delicious gluten-free chocolate chip muffins, use yogurt + oil in the batter! Read on for more tips on making amazing gluten-free muffins.

A gluten-free chocolate chip muffin on a counter


 

Want to make gluten free chocolate chip muffins that are soft, tender, and delicious? You’ve come to the right place! This muffins are tried and tested, ensuring they turn out perfect every time.

These healthy chocolate chip muffins check every box for a winning recipe. They’re tender, fluffy muffins made with wholesome ingredients.

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

No one will ever guess they’re gluten-free, thanks to the best gluten-free flour, oil, and whole milk yogurt.(You also might like these gluten-free apple muffins!)

This is one of those quick, easy recipes made with pantry staples. You’ll get bakery-style muffins with tall muffin tops and a shiny, sugary appearance. And most importantly, this is a gluten-free muffin recipe the whole family is guaranteed to love.

The gluten free chocolate chip muffin recipe is also versatile enough to customize the muffins any way you’d like.

Throw in regular or mini chocolate chips or dark chocolate chunks. Add extra mix-ins like orange zest or peanut butter chips, or bake them in a mini muffin pan for the cutest mini muffins!

Table of Contents

Why You’ll Love this Recipe

  • Tender, fluffy crumb
  • Makes perfect muffins every time
  • Can be customized with other add-ins
  • Made with pantry staples
  • Can be made in less than an hour

For more tasty treats, try these gluten-free chocolate chip cookies or these baked gluten-free donuts!

Ingredients You’ll Need

These gluten-free muffins are made with easy-to-find pantry staples. This recipe is based on my tried-and-true master recipe for gluten-free muffins.

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!

gluten-free chocolate chip muffin ingredients laid out on a countertop
  • Gluten-Free 1:1 Baking Flour: These bakery style muffins turn out best when you use a high-quality 1:1 gluten-free baking flour. Look for a gluten-free flour blend that contains xanthan gum so the muffins have the structure they need. King Arthur is my favorite brand but I also like Bob’s Red Mill!
  • Almond Flour: I love adding a little almond flour to my gluten-free baked goods for moisture and richness. I love adding part almond flour to my gluten-free banana bread!
  • 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. You could also use sour cream in place of the yogurt.
  • Oil: These muffins call for oil instead of butter. As much as I love melted butter, I find that oil makes for a fluffier texture in gluten-free cakes and muffins. This is because oil melts faster than butter and coats the dry ingredients more quickly during baking to create an even texture. You can use any kind of oil – canola oil, vegetable oil, coconut oil or even avocado oil in this recipe.
  • Sugar: I use granulated cane sugar for this recipe. The muffins won’t turn out as light and fluffy (and will have a darker color) if you use coconut sugar.
  • Eggs: Eggs are crucial for the structure of these muffins. I do not recommend using flax eggs. To try these egg-free I would try Bob’s Red Mill Egg replacer.
  • Lemon Juice: Lemon juice not only adds a nice zing to the muffins and helps tenderize the the crumb.
  • Mix-Ins: There are endless mix-in options for these muffins!

Check out this post on are chocolate chips gluten-free.

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.

How to Make Gluten-Free Chocolate Chip Muffins

A muffin tin with cupcake liners, a bowl of dry ingredients, and a mixer with the muffin batter inside
  • Preheat the oven to 425F. Line a standard muffin tin with muffin liners.
  • In a medium or large bowl, whisk together the dry ingredients. Set aside.
  • In the bowl of a stand mixer fitted with a paddle attachment, add sugar and room temperature eggs. 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 vanilla extract and mix.
A mixer stirring up the muffin batter
  • Now it’s time to combine the wet ingredients with the dry ingredients. 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 muffin batter is totally smooth.
Chocolate chip muffin batter in a mixing bowl with a spatula
  • Stir in the chocolate chips with a rubber spatula.
  • Using a kitchen scoop or large spoon, divide batter evenly into the cupcake liners in the prepared muffin tin.
chocolate chip muffin batter in the 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!

Storage/Freezing Instructions

To store: After the gluten-free chocolate muffins have cooled on the cooling rack, you can store muffins with their paper liners in an airtight container for up to three days.

To freeze: 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. 

Muffin FAQs

How do you make gluten-free muffins rise?

You can make gluten-free muffins rise by setting the oven to a higher temperature for the first 10 minutes of baking.

Are chocolate chips gluten-free?

Most chocolate chips are gluten-free, but it’s always best to check the labeling to ensure the specific brand you choose is free of gluten!

Why are my gluten-free muffins dry?

It’s important to use whole milk yogurt and a high-quality gluten-free flour to prevent muffins from being crumbly and dry.

Expert Tips and Tricks

  • Sprinkle the muffins with a little raw sugar before baking to give them a professional, sparkly muffin top!
  • If you decide to add other mix-ins, don’t add more than one cup. Gluten-free muffins have a more delicate structure!
  • You could also adding a crumb topping to your muffins, as found in my gluten-free orange cranberry muffins.
a gluten-free muffin broken in half

More Gluten-Free Muffin/Quick Bread Recipes

Happy baking! I hope this guide helps you make beautiful muffins. If you make this recipe, please leave me a comment/rating below! I’d love to hear from you!

A gluten-free chocolate chip muffin
5 from 10 votes

Gluten-Free Chocolate Chip Muffins (Best Ever!)

Prep Time 20 minutes
Cook Time 20 minutes
Total Time 40 minutes
Servings 12 muffins
These gluten-free chocolate chip muffins are a recipe you'll come back to time and time again. They're a bakery-style treat you can whip up for breakfast, brunch, parties, or an afternoon snack.

Video

Ingredients

Dry Ingredients

  • 1 ½ cups gluten-free 1:1 baking flour
  • ½ cup almond flour (or ⅓ cup more gluten-free 1:1 baking flour)
  • 1 ½ teaspoons baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon kosher salt
  • ¼ teaspoon nutmeg
  • ¼ teaspoon cinnamon

Other Ingredients

  • 2 large eggs
  • cup sugar
  • ½ cup vegetable oil or oil of choice
  • 1 teaspoon lemon juice
  • 1 teaspoon vanilla extract
  • 1 cup whole-milk yogurt
  • ¾ cup mini chocolate chips
  • Raw sugar for topping 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 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.) Add the lemon juice and vanilla extract 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 chocolate chips with a rubber spatula. Using a kitchen scoop or large spoon, portion the batter evenly into the 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

  • Sprinkle the muffins with a little raw sugar before baking to give them a professional, sparkly muffin top!
  • If you decide to add other mix-ins, don’t add more than one cup. Gluten-free muffins have a more delicate structure!
  • You could also adding a crumb topping to your muffins, as found in my gluten-free orange cranberry muffins.

Nutrition

Calories: 211kcal | Carbohydrates: 31g | Protein: 5g | Fat: 8g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 1g | Cholesterol: 32mg | Sodium: 173mg | Potassium: 149mg | Fiber: 2g | Sugar: 19g | Vitamin A: 85IU | Vitamin C: 1mg | Calcium: 82mg | 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. I have made these muffins numerous times and they are always amazing!

    Quick question, I don’t always have whole milk yogurt on hand. Can the yogurt be replaced with sour cream?

  2. 5 stars
    These muffins are delicious! I can see myself making these frequently for our family of 8! Thank you for developing gluten free recipes that are delicious (and nutritious)!

  3. 5 stars
    these muffins are the best gluten free muffins I have made so far! thank you so much for sharing this amazing recipe!

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