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    Home » Recipes » Gluten Free Dessert Recipes

    Gluten Free Chocolate Chip Muffins (Bakery Style)

    Last Modified: Jun 12, 2025 by Chelsea Joy · This post may contain affiliate links · This blog generates income via ads

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    These Gluten Free Chocolate Chip Muffins boast big, golden-brown domes that are soft and fluffy inside - the perfect bakery-style gluten free muffin!

    This recipe has been a huge labor of love, going through multiple tests to find the right measurements for crave-worthy muffins.

    And here they are!

    Closeup of gluten free chocolate chip muffins on a tray

    Your new favorite gluten free muffins

    Fluffy, golden-brown, and huge - that's what these gluten free chocolate chip muffins are all about!

    There aren't many culinary pleasures I enjoy more than a rich baked good paired with coffee, and this recipe definitely hits the mark.

    This gluten free muffin recipe is straightforward, doesn't require an extensive ingredient list, and hot dang are they delicious.

    Despite their size, eating ONLY one is a challenge!

    Even my non-gluten free friends happily gobbled up my final test batch... and asked for seconds. That's a win!

    Jump to:
    • Your new favorite gluten free muffins
    • Ingredient notes for gluten free chocolate chip muffins
    • Tips for bakery-style muffins
    • FAQs
    • More gluten free baking recipes to try
    • 📖 Recipe

    Ingredient notes for gluten free chocolate chip muffins

    It was important to me to make a winning gluten free muffin recipe withOUT using a special homemade gluten free flour blend or incorporate a bunch of uncommon ingredients.

    I experimented with some of my go-to storebought gluten free flour blends, and hit on one as a favorite.

    Beyond that, the ingredients in these muffins are fairly straightforward. Let's dive in!

    GLUTEN FREE FLOUR - My favorite blend for virtually all my gluten free baking projects is Bob's Red Mill 1:1 Baking Flour.

    You can find it in almost every grocery store, it works well for a variety of baking, and it already contains xanthan gum (an important ingredient in gluten free baking.)

    BUTTER - Melted and cooled, it's hard to make an argument for NOT including butter in a baked goods recipe, particularly if you are looking for a true, rich treat. No "healthified" versions on this page!

    Overhead view of bakery-style gluten free chocolate chip muffins

    EGGS - After testing these muffins a couple times, they clearly needed a little more lift and structure. Without gluten, it's simply more challenging to create the fluffy structure we love in baked goods.

    Using one more egg than you might be used to finding in a muffin recipe creates a little more structure!

    LEMON JUICE + BAKING POWDER - Without gluten, baked goods need a little additional help with lift. The combination of a little extra baking powder and lemon juice (or apple cider vinegar) creates a chemical reaction that creates LIFT! That's what makes the big, beautifully-domed muffins that are soft and fluffy inside. Hooray!

    GREEK YOGURT - This ingredient serves a couple different purposes. Low-fat Greek yogurt helps keep these muffins moist, while the natural acidity works with baking powder to help with that lift.

    You can substitute sour cream for Greek yogurt if you'd like. I fell in love with this trick when developing Gluten Free Cranberry Orange Scones!

    TURBINADO SUGAR: A sprinkling of turbinado sugar before baking helps brown the muffins and creates that almost-crackly texture for the muffin top.

    Closeup of a gluten free chocolate chip muffin with a beautifully-domed golden brown top

    Tips for bakery-style muffins

    - Batter should be thick

    The batter for these muffins should be pretty thick! If you are worried it's too thick, trust the process.

    However, if it is SO thick that you can't plop it into the muffin liners, you may need to add some additional milk to thin out the batter.

    - Lots of leavening for beautifully-domed tops

    As mentioned in the ingredient notes, gluten free baked goods need a little extra help to create the structure and fluffiness we want in our sweet pastries.

    So for these gluten free chocolate chip muffins, I employed several strategies to get the lift needed.

    Using both baking soda and baking powder, adding lemon juice or apple cider vinegar, and leaning on the acidity in Greek yogurt or sour cream all help in this department.

    - Don't overmix!

    Overmixing the batter leads quickly to tough, not fluffy muffins.

    Mix the batter just until all the ingredients are combined. For this reason, I don't suggest using an electric mixer.

    Muffin batter ready to bake in a muffin tin

    - Fill the muffin liners to the top

    Want to get those big, beautiful, bakery-style muffin tops? Fill those muffin liners, baby!

    General advice suggests filling ¾ full, but this recipe will ask you to fill them to the top. Trust me, you'll love the results!

    - Only use half the muffin tin

    Because we're filling those muffin liners to the top and we want the domes to lift and spread beyond their boundaries, you'll leave half the tin empty. Skip every other indent to give the domes room to grow without bumping up against each other.

    A gluten free chocolate chip muffin torn open on a small plate, surrounded by chocolate chips and more muffins

    FAQs

    My muffins didn't rise. What happened?

    Usually expired baking soda or baking powder are to blame for baked goods that don't rise. We often keep these ingredients around in perpetuity without checking whether they still work!

    To test if your baking soda or powder are fresh, put ¼ teaspoon soda or powder in a cup and add a small amount of vinegar or very hot water. If it doesn't bubble, it should be replaced.

    Can I use other mix-ins in place of chocolate chips?

    Sure, if the ingredients aren't too acidic! Swapping in fresh/frozen berries or nuts should work fine.

    More gluten free baking recipes to try

    While a lot of my meals are macro-friendly, I definitely think we all need a sweet treat once in a while! I have several decadent gluten free baking recipes on Chelsea Joy Eats.

    Give our house-favorite Gluten Free Hummingbird Cake a try! Or for a more classic cake, grab Gluten Free Carrot Cake with Cream Cheese Frosting.

    Cookie fans, I've got you: GF White Chocolate Macadamia Nut Cookies are my husband's favorite cookies, hands down.

    Or whip up a Apple Skillet Cake with Walnuts (Gluten Free) for another baked good that goes great with coffee, like these muffins.


    Have you made a batch of these gluten free chocolate chip muffins? I'd love to hear what you think! Comment below or tag me on Instagram.

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    📖 Recipe

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    Gluten free chocolate chip muffins stacked on top of one another

    Gluten Free Chocolate Chip Muffins

    5 Stars 4 Stars 3 Stars 2 Stars 1 Star No reviews
    • Author: Chelsea Joy
    • Prep Time: 35 minutes
    • Cook Time: 22 minutes
    • Total Time: 57 minutes
    • Yield: 12 muffins 1x
    • Category: Dessert
    • Method: Baked
    • Diet: Gluten Free
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    Description

    These gluten free chocolate chip muffins have the big, golden-brown domes that catch your eye at your local coffee shop, plus soft, fluffy insides - the perfect bakery-style muffin! And no one would guess they're gluten free.


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    Ingredients

    Units Scale
    • 3 cups gluten free 1:1 flour, spooned and leveled (I use Bob's Red Mill gluten free 1:1 flour)
    • 1 cup cane sugar
    • 2 teaspoons baking powder
    • 1 teaspoon baking soda
    • ¼ teaspoon ground cinnamon
    • ¼ teaspoon ground nutmeg
    • 1 teaspoon fine sea salt
    • 8 tablespoons butter, melted and cooled to room temperature
    • ½ cup plain low-fat yogurt or sour cream, room temperature
    • ½ cup milk
    • 3 large eggs, room temperature
    • 1 teaspoon vanilla extract
    • 2 tablespoons lemon juice
    • 1 ½ cups chocolate chips (I use Enjoy Life)
    • 2-3 tablespoons turbinado or cane sugar, for topping

    Instructions

    1. In a mixing bowl, combine the flour, sugar, baking powder, baking soda, cinnamon, nutmeg, and sea salt. Stir with a spoon or whisk to fully incorporate ingredients and set aside.
    2. In a larger mixing bowl, combine the butter, yogurt, eggs, vanilla extract, and lemon juice. Whisk until smooth. 
    3. Gradually mix the dry ingredients into the wet ingredients until a batter is formed - don't overmix, or you'll end up with chewy muffins. Pour in 1 ½ cups chocolate chips and mix just  until combined. Cover the bowl with a tea towel, lid, or wrap and let rest for at least 30 minutes and up to an hour. Meanwhile, move one oven rack to the middle position and preheat the oven to 425 degrees F.
    4. For bakery-style muffins, line a 12-count muffin pan with 6 muffin liners (this leaves room for those extra-big domed tops - meaning you'll have to bake in 2 batches). Fill the liners with about ½ cup of batter, so the batter rests just above the liner. Top the muffins with extra chocolate chips, if desired, and sprinkle with coarse sugar.
    5. Place one pan in the center of the oven and bake for 7 minutes at 425 degrees F, then (without opening the oven door) decrease the temperature to 350 degrees F and bake for an additional 12-15 minutes or until a toothpick inserted in the center comes out clean. Allow the muffins to cool for a couple minutes before removing to a wire rack. Repeat with the remaining batter, starting with the oven at 425 degrees F. Let cool completely before eating.

    Did you make this recipe?

    Leave a comment and rating below or tag @chelseajoyeats on Instagram!

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    Woman in athletic wear leaning on a kitchen counter while holding a cup of coffee

    Hello! I'm Chelsea, the sole author, recipe developer, and photographer behind Chelsea Joy Eats.

    Life should be full of flavor! I've made it my mission to bring you healthy, often high protein and gluten free recipes while also venturing into indulgent desserts. Want to know more?

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