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    Home » Breakfast

    Gluten Free Chocolate Muffins

    Updated: Apr 2, 2025 by Tiffany · This post may contain affiliate links · Leave a Comment.

     

     

    Jump to Recipe Print Recipe

    Last week my chocolate hating son went away on a school trip, so I was free to indulge my chocolate addiction all week long.  The first thing I baked were these gluten free chocolate muffins. Then, I promptly baked a second batch!

    These bakery-style muffins are extra tender thanks to the addition of sour cream and they're absolutely filled with rich chocolate flavor. If you're a chocolate lover like me, they're the perfect start to the day!

    Several gluten free chocolate muffins sitting on a wood tray.

    If you love gluten-free chocolate chip muffins, you should try my gluten free banana chocolate chip muffins or these extra moist zucchini chocolate chip muffins.

    Jump to:
    • Ingredient Notes
    • Substitutions & Variations
    • How to make Gluten-Free Chocolate Muffins
    • Expert Tip
    • How to Get Perfect Gluten Free Muffins
    • Storage
    • More gluten-free muffins to consider:
    • Recipe

    Ingredient Notes

    These delicious muffins use just a few simple ingredients and it's both gluten free and dairy free.

    Ingredients for gluten free chocolate muffins sitting on a marble counter.
    • Gluten-Free Flour Blend - I use Bob's Red Mill 1-to-1 Flour Blend for all of my muffin recipes.  You can use the gluten free flour blend of your choice, but ensure it contains xanthan gum or a similar binder.  I don't recommend a single flour replacement, like almond flour.  
    • Unsweetened Cocoa Powder - This recipe uses natural cocoa powder, like Hershey's unsweetened cocoa powder.  Do NOT substitute Dutch process cocoa.  
    • Vegan Sour Cream - My two favorite brands of dairy free sour cream are Forager brand and Follow Your Heart.  I'm sure any brand of vegan sour cream will work fine.  And if you're not dairy free, just use regular sour cream in the same measure. 
    • Non-Dairy Milk - I use unsweetened coconut milk or oat milk in all of my recipes, but I'm sure any kind of dairy free milk alternative will work.  If you're not dairy free, use whole milk in the same measure. 
    • Dairy-Free Chocolate Chips - I typically use either Enjoy Life Brand or Nestle Allergen Free chocolate chips.  I used semi-sweet chocolate chips for this recipe (dairy free of course).  But I think they would also be delicious with chocolate chunks, milk chocolate chips or even white chocolate chips.

    See recipe card for full ingredient list and quantities.

    Substitutions & Variations

    • Not Dairy Free - use dairy sour cream and milk in the same measure.
    • Chocolate Switchup - Replace the semi-sweet chocolate chips with dark chocolate chips, dairy free white chocolate chips or peanut butter chips.
    • Get Nutty - Replace half of the chocolate chips with ½ cup of chopped nuts. I think pecans would be delicious in this recipe.
    • Muffin Sizes - make approximately 36 mini muffins (I would recommend mini chocolate chips here) or 4 jumbo sized muffins. You could also bake this recipe in a loaf pan to make a chocolate quick bread.

    How to make Gluten-Free Chocolate Muffins

    As with all of my gluten-free muffin recipes, I use the muffin method for these double chocolate muffins.  It's super easy and does not require a mixer.  Plus, it always yields beautiful tall muffin tops. 

    Before you begin mixing, line a 12 cup muffin pan with paper liners.

    Dry ingredients in a large glass mixing bowl.

    STEP 1: Combine the gluten free flour, cocoa powder, sugar, brown sugar, baking powder, baking soda, and salt in a large mixing bowl.  Whisk to mix well.

    Two eggs beaten in a small glass bowl.

    STEP 2: Crack the eggs into a separate bowl and beat the with the whisk until they're frothy like soap bubbles.

    Sour cream, milk, oil and vanilla being mixed into the bowl with the beaten eggs.

    STEP 3: Add the sour cream, milk, oil, and vanilla extract to the bowl with the beaten eggs.  Whisk again until smooth.

    Wet ingredients being poured into the mixing bowl with the dry ingredients.

    STEP 4: Pour the wet ingredients into the bowl with the dry ingredients.  Fold together with a spatula for about 10 strokes.

    Chocolate chips being mixed into the chocolate muffin batter.

    STEP 5: Add the chocolate chips to the muffin batter and fold together about 5 more strokes.  The batter will be thick, but don't worry. 

    Use an ice cream scoop to portion the batter into your prepared muffin tin.  Let the batter rest for 10 minutes, then bake.

    Expert Tip

    To check for done, gently poke the top center of a muffin.  If the top springs right back, the muffins are fully baked.  If your finger leaves an indentation, bake for another 2 minutes and check again.

    Freshly baked gluten free chocolate muffins in a muffin tin sitting on a wooden cutting board.

    How to Get Perfect Gluten Free Muffins

    There are four parts to getting a really nicely domed muffin top.

    • Use the muffin method for mixing.  This allows the eggs to create air bubbles which then grow larger once the baking powder is activated.
    • Fill your muffin cups nearly to the top.  Lots of recipes call for filling a muffin cup ½ or ⅔ full, but those will result in flat tops.  
    • Start with a high baking temperature.  By baking muffins at a higher temperature than cake for example, the outer edge of the muffin sets quickly and pushes the center up as it continues to bake.
    • Cook for the appropriate time.  If you take your muffins out of the oven too soon, the tops may fall leaving a flat or indented muffin top.
    • Allow the baked muffins to sit in the muffin pan for no longer than 10 minutes after they are out of the oven.  Then move them to a wire rack to cool.

    Storage

    Store leftover muffins in an airtight container lined with a paper towel. They can be stored at room temperature for up to 4 days.

    A gluten free chocolate muffin cut open showing the melted chocolate chips inside.

    More gluten-free muffins to consider:

    • A batch of gluten free orange poppy seed muffins sitting on a wood cutting board.
      Orange Poppy Seed Muffins
    • Several banana oat flour muffins sitting on a wooden tray.
      Oat Flour Banana Muffins
    • Several cranberry sauce muffins served on a ceramic plate.
      Cranberry Sauce Muffins
    • Freshly baked gluten free blackberry muffins sitting on a plate with a few fresh blackberries.
      Gluten Free Blackberry Muffins

    If you try this recipe, please leave a 🌟🌟🌟🌟🌟 star rating and let me know how you liked it in the comments below.

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    Recipe

    Several gluten free chocolate muffins sitting on a wood tray.

    Gluten Free Chocolate Muffins

    These amazing gluten free chocolate muffins are a chocolate lover's dream! Filled with loads of chocolate flavor and gooey chocolate chips, they are the perfect way to enjoy chocolate for breakfast!
    Author: Tiffany
    No ratings yet
    Print Pin Go Ad Free
    Course: Breakfast
    Cuisine: American
    Prep Time: 10 minutes minutes
    Cook Time: 27 minutes minutes
    Resting Time: 10 minutes minutes
    Total Time: 47 minutes minutes
    Servings: 12
    Calories: 344kcal
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    Ingredients

    • 1 ⅔ Cups Gluten Free 1-to-1 Flour Blend I use Bob's Red Mill
    • ½ Cup Unsweetened Cocoa Powder
    • ¾ Cup Sugar
    • ½ Cup Brown Sugar
    • 1 ½ teaspoons Baking Powder
    • ½ teaspoon Baking Soda
    • ½ teaspoon Salt
    • 2 Eggs
    • ½ Cup Vegan Sour Cream
    • ½ Cup Non Dairy Milk
    • 6 Tablespoons Oil
    • 2 teaspoons Vanilla
    • 1 Cup Allergen Free Semi-Sweet Chocolate Chips
    US Customary - Metric

    Instructions

    • Preheat oven to 400 °F (204 °C). Line 12 muffin cups with paper liners.
    • Combine the gluten free flour, cocoa powder, sugar, brown sugar, baking powder, baking soda and salt in a large mixing bowl. Whisk to mix well. Set aside.
      1 ⅔ Cups Gluten Free 1-to-1 Flour Blend, ½ Cup Unsweetened Cocoa Powder, ¾ Cup Sugar, ½ Cup Brown Sugar, 1 ½ teaspoons Baking Powder, ½ teaspoon Baking Soda, ½ teaspoon Salt
    • Crack the eggs into a separate bowl and whisk them until they are frothy like soap bubbles.
      2 Eggs
    • Add the sour cream, oil, milk, and vanilla to the eggs and whisk until well combined.
      ½ Cup Vegan Sour Cream, ½ Cup Non Dairy Milk, 6 Tablespoons Oil, 2 teaspoons Vanilla
    • Pour the wet ingredients into the dry ingredients and fold together with a rubber spatula for about 10 strokes.
    • Add the chocolate chips and fold for 5 more strokes.
      1 Cup Allergen Free Semi-Sweet Chocolate Chips
    • Divide the muffin batter into your prepared muffin tin. Let it rest for 10 minutes at room temperature. Sprinkle the tops with a few extra chocolate chips.
    • Bake in the preheated oven for 5 minutes, then reduce the oven temperature to 350 °F (177 °C) and have for an additional 20-22 minutes or until the tops spring back when gently poked.
    • Remove the muffins from the oven and allow them to cool in the pan for 10 minutes. Then transfer them to a cooling rack.

    Notes

    STORAGE: Store leftover muffins in an airtight container lined with a paper towel. They can be stored at room temperature for up to 4 days.
    Calories: 344kcal | Carbohydrates: 48g | Protein: 5g | Fat: 17g | Saturated Fat: 5g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 7g | Trans Fat: 0.04g | Cholesterol: 28mg | Sodium: 267mg | Potassium: 179mg | Fiber: 4g | Sugar: 29g | Vitamin A: 86IU | Vitamin C: 1mg | Calcium: 81mg | Iron: 2mg
    Tried this recipe?Mention @wellfedbaker or tag #wellfedbaker!
    Tiffany

    Tiffany is the recipe developer, stylist and food photographer behind Well Fed Baker. As a lifelong baker who had to go gluten free and dairy free in 2016, Tiffany strives to share allergen friendly recipes that never feel like they are free from anything.

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    Hey, I'm Tiffany!

    I love sharing gluten-free comfort food and homestyle baking, featuring Dutch oven meals, nostalgic dinners, classic baked goods, with dairy-free or allergen-friendly options. My recipes lean Southern, seasonal, and practical.

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