Gluten-Free Double Chocolate Muffins

These gluten-free double chocolate muffins are what every chocolate lover dreams of – soft, rich, and filled with melty chocolate chips in every bite. They’re made with simple gluten-free pantry staples and come together in one bowl (so yes, minimal clean-up too!).

gluten-free double chocolate chip muffins

Why These Are The Gluten-Free Chocolate Muffins to Make

If you’ve ever been let down by dry or crumbly gluten-free muffin recipes before, this one will change that. They bake up tall, fluffy, and soft – never dry – and the double hit of cocoa and chocolate chips means every bite tastes like dessert. I like to keep a batch in the freezer so I can swap them in whenever non-gluten-free muffins show up – no one feels left out, and my kids get the same chocolatey joy as everyone else.

You’ll love them because they’re:

  • 🍫 Double chocolate bliss – cocoa + chocolate chips = perfection
  • 🧁 Soft, fluffy, and moist – thanks to yogurt and oil
  • 🥣 One bowl & no mixer required
  • 🧊 Freezer-friendly
  • 👩‍🍳 Reliable – they rise beautifully and stay soft
Close-up of a moist gluten-free chocolate muffin

Ingredients to Make Gluten-Free Double Chocolate Muffins

Here’s what you’ll need:

  • 2 large eggs
  • ½ cup sugar – brown sugar adds softness and depth, but you can also use white sugar if preferred.
  • ½ cup oil – neutral oil such as vegetable or canola work well.
  • 1 cup plain or Greek yogurt – keeps these muffins soft and tender.
  • 2 tsp vanilla extract
  • 1½ cups gluten-free all-purpose/plain flour – use a blend with xanthan gum if possible (or add 3/4 tsp of xanthan gum).
  • ⅓ cup unsweetened cocoa powder – natural cocoa gives a balanced chocolate flavor.
  • 2 tsp gluten-free baking powder
  • ½ tsp baking soda
  • ¼ tsp salt
  • 1 cup chocolate chips – milk, dark, or a mix of both.
  • (Optional): 1 tsp instant coffee or espresso powder – helps to deepen the chocolate flavor, but doesn’t leave a ‘coffee’ taste.
Ingredients to make Gluten-Free Double Choc Muffins

Greek vs Plain Yogurt – Which Is Better?

Both work beautifully – just don’t skip the yogurt!

  • Greek yogurt: richer and thicker, for a fudgier muffin.
  • Plain yogurt: lighter, for a softer, more cake-like texture.

If using thick Greek yogurt, you can stir in 1 to 2 tbsp milk if the batter looks a bit stiff.

Substitutions & Alternatives

  • Dairy-free: Use coconut or soy yogurt and dairy-free chocolate chips.
  • Egg-free: Replace each egg with a flax egg (1 tbsp flaxseed meal + 3 tbsp water).
  • Nut-free: Naturally nut-free – just check your chocolate chips!
  • Extra chocolate boost: Add 1 tsp espresso powder to enhance the cocoa flavor.
gluten-free double chocolate muffins

How To Make Gluten-Free Chocolate Chocolate Chip Muffins – Step by Step

Step 1: Preheat oven to 175°C (350°F). Line or lightly grease a 12-hole muffin tray.

Step 2: In a large bowl, whisk together 2 large eggs½ cup neutral oil1 cup plain or Greek yogurt2 tsp vanilla extract and ½ cup brown sugar until smooth.

whisk together the wet ingredients of gluten-free double chocolate muffins

Step 3: Add 1½ cups gluten-free all-purpose/plain flour ⅓ cup unsweetened cocoa powder2 tsp gluten-free baking powder½ tsp baking soda and ¼ tsp salt. Stir gently until just combined, but don’t overmix!

add the dry ingredients to make gluten-free chocolate muffins

Step 4: Fold in ¾ cup chocolate chips (and espresso powder if using), reserving a few for topping.

Fold in ¾ cup chocolate chips

Step 5: Spoon batter into muffin cups and top with extra chocolate chips. Bake for 18 to 20 minutes (check at 18 minutes) or until a toothpick inserted comes out with moist crumbs.

fill muffin liners

Step 6: Cool for 5 minutes in the pan, then transfer to a wire rack.

gluten-free double chocolate chip muffins

How To Store and Freeze Gluten-Free Chocolate Muffins

  • Store: Keep in an airtight container at room temperature for up to 3 days – may need 15 seconds in the microwave to ‘spruce’ them up again by day 3 though!
  • Freeze: Freeze for up to 3 months. Thaw overnight.
double chocolate muffins gluten-free

Optional Toppings or Mix-Ins

  • Add white chocolate chips for a triple-chocolate version.
  • Stir through raspberries or cherries for a fruity twist.
  • Sprinkle with mini chocolate chips or sea salt flakes before baking.
  • Drizzle cooled muffins with melted chocolate for a bakery-style finish.

Troubleshooting Common Issues

  • Dry muffins? Cocoa can absorb moisture so be sure to measure your 1/3 of a cup well, and avoid overbaking.
  • Flat tops? Check that your baking powder and soda are fresh.
  • Dense texture? Mix only until just combined – gluten-free batters don’t like to be overworked.
gluten-free chocolate chocolate chip muffin recipe

Gluten-Free Double Chocolate Muffins

These gluten-free double chocolate muffins are soft, rich, and packed with chocolate chips. Made in one bowl with pantry staples, they’re a quick and easy gluten-free delight.
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Gluten-Free Snack
Gluten-Free Family
Gluten-Free Muffins
Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes
Servings: 12 muffins

Equipment

  • Mixing bowl
  • Muffin baking tray
  • Oven

Ingredients 

Wet Ingredients:

  • 2 large eggs
  • ½ cup neutral oil (vegetable, canola, or light olive)
  • 1 cup plain or Greek yogurt (whole-milk)
  • 2 tsp vanilla extract
  • ½ cup brown sugar

Dry Ingredients:

  • cups gluten-free all-purpose/plain flour (check xanthan gum is included, otherwise you will need to add ¾ tsp xanthan gum)
  • cup unsweetened cocoa powder
  • 2 tsp gluten-free baking powder
  • ½ tsp baking soda
  • ¼ tsp salt
  • ¾ cup chocolate chips
  • (Optional) 1 tsp instant coffee or espresso powder

Instructions

  • Preheat oven to 350°F (175°C). Line a 12-hole muffin tin with liners and lightly spray with oil.
  • In a large bowl, whisk together 2 large eggs, ½ cup neutral oil, 1 cup plain or Greek yogurt, 2 tsp vanilla extract and ½ cup brown sugar until smooth.
  • Add 1½ cups gluten-free all-purpose/plain flour , ⅓ cup unsweetened cocoa powder, 2 tsp gluten-free baking powder, ½ tsp baking soda and ¼ tsp salt. Stir gently until just combined.
  • Fold in ¾ cup chocolate chips (and espresso powder if using), reserving a few for topping.
  • Spoon batter into muffin cups and top with extra chocolate chips.
  • Bake for 18 to 20 minutes (check at 18 minutes) or until a toothpick inserted comes out with moist crumbs.
  • Cool for 5 minutes in the pan, then transfer to a wire rack.

Recipe Notes:

Approximate baking times:

  • 🧁 12 standard muffins: 18-20 minutes
  • 🧺 6 large café-style muffins: 23-26 minutes
  • 🎉 24 mini muffins: 11-13 minutes
Every oven varies slightly, so start checking a couple of minutes before the lower time – muffins are ready when the tops spring back when lightly pressed.

Storage:

Store muffins in an airtight container lined with paper towel (top and bottom) for up to 2 days, or freeze individually for up to 2 months.

Nutrition Information:

Calories: 250kcal | Carbohydrates: 29g | Protein: 5g | Fat: 14g | Saturated Fat: 4g | Polyunsaturated Fat: 5g | Monounsaturated Fat: 3g | Trans Fat: 0.1g | Cholesterol: 28mg | Sodium: 184mg | Potassium: 115mg | Fiber: 2g | Sugar: 17g | Vitamin A: 40IU | Calcium: 91mg | Iron: 1mg

Did you make this recipe?

Mention us @theglutenfreekids or tag us using #theglutenfreekids so we can see your creations! You can also leave a comment below!

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