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  • Gluten Free
  • Vegetarian

How to Make Gluten-Free Double Chocolate Muffins

These bakery-style muffins are moist, rich, decadent, and so chocolatey! And they’re gluten-free! The healthy, easy-to-make gluten-free double chocolate muffins will easily become your favorite.

gf chocolate muffins with chocolate chips

I absolutely love muffins and they’re part of my sweet ways to enjoy life. I could eat muffins every single day if I wanted to – seriously there is no such thing as too many muffins. If someone is telling you it’s too early for muffins, walk away – with a muffin in hand because life is too short, and muffins are way too delicious.

Now my whole family has their own favorite kind of muffin. From blueberry to carrot cake, we don’t discriminate in this house. We make and eat all of them. But there’s something extra special about chocolate muffins. A quick muffin in the morning is basically like eating dessert for breakfast – but healthier.

You guys, these fluffy, super tasty, and tender muffins will not disappoint. They are perfectly textured, moist, and so good! The best part? These gluten-free double chocolate muffins recipe is made with healthier ingredients such as almond meal, cacao powder, and coconut oil. And topped with chocolate chips for added sweetness and that double chocolate punch making them perfect for chocolate lovers. 

These gorgeously sweet, rich, scrumptious, easy-to-make chocolate chip muffins can be enjoyed for breakfast, lunch, or as a snack. The healthy chocolate muffins are best enjoyed warm but can easily be reheated if you’re lucky to have leftovers. 

Key Ingredients

GF Chocolate Muffins 1172x2000

Almond Meal: This is slightly different from almond flour. While almond flour is made from peeled and blanched almonds, almond meal is made using raw almonds. It is darker in color and has a more pronounced almond flavor. Almond meals and almond flour are both great alternatives to traditional flour if you’re looking to create a gluten-free recipe.

Cacao Powder: Cacao powder provides that rich chocolatey taste with even more added benefits. It’s packed with flavonoids which can lower blood pressure, reduce the risk of diabetes, and even improve blood flow to the brain.

Baking Soda: To get a great lift in the muffins and helps to brown your muffins in the oven. If you don’t like the soda taste, substitute to baking powder.

Sea Salt: Just a touch to balance out the flavors.

Eggs: 2 whole eggs will give you the perfect texture to make a moist, tender, and fluffy muffin. 

Maple Syrup: A great, mild yet flavorful liquid sweetener.

Coconut Oil:  A healthier alternative to most other vegetable oils, coconut oil provides a neutral taste so the rich chocolate flavor can really shine here. You can also use unsalted butter instead.

Vanilla Extract: Just a splash for flavor.

And of course, Chocolate Chips to make the double chocolatey flavor. 

Find the full printable recipe with specific measurements below.

How to Make Gluten-Free Double Chocolate Muffins

Step 1: Oven and Muffin Pan preparation 

Preheat oven to 350°F then line a 12-cup muffin tin with muffin liners.

Step 2: Combine the dry ingredients

In a large bowl, mix the dry ingredients (almond meal, cocoa, baking soda, salt) until they’re evenly combined and set aside.

gf cocoa dry ingredients mix

Step 3: Heat oil and syrup

In a small pot over medium-low heat, gently melt coconut oil. Whisk in maple syrup. Allow the mixture to cool on the stove for a few minutes.

gf muffins syrup mix

Step 4: Combine wet ingredients 

Next, combine the eggs and vanilla extract in a separate bowl. Add coconut oil until it’s fully incorporated then add maple syrup to the egg mixture and whisk well.

gf chocolate muffins batter

Step 5: Make the muffin batter 

Slowly add the wet ingredients to the dry ingredients and stir until just mixed. Don’t overmix the batter. 

gf chocolate batter mix

Step 6: Add the chocolate chips

Fold in the chocolate chips until they’re dispersed and everything is combined evenly. Again, don’t over mix the batter. 

Step 7: Fill muffin tins

Transfer the muffin batter to the muffin tins and fill them until they’re 3/4 full so that the muffins don’t spill over the sides as they bake. 

gf muffins chocolate muffins

Step 8: Bake muffins

Bake for 15-20 minutes or until tops are set (timing depends on the oven, make sure muffin tops are slightly firm to touch before removing from oven). You can insert a toothpick in the center and if it comes out clean or with dry crumbs, you’re good to go. 

gf chocolate muffins baked

Step 9: Cool and serve

Once done, remove from oven and allow muffins to cool in the pan for 15 minutes then transfer to a wire rack so they cool completely. Serve warm. 

gluten free chocolate chip muffins

Expert Tips

  • Bake with ingredients that are at room temperature because it helps the muffin batter blend together well. Cold ingredients can make the batter lumpy. 
  • You can substitute maple syrup with honey, agave, or sugar-free syrup.
  • For uniformed-sized muffins, use an ice cream scoop. It makes it nice and easy to get the perfect amount in the muffin pan. 
  • Sprinkle the tops with additional chocolate chips if you’d like. 

How to store the gluten-free chocolate muffins

You can store the healthy chocolate muffins at room temperature in an airtight container or ziplock bag for up to 3 days. If you put them in the refrigerator, they can stay for 5-7 days.  Place them in a single layer then put a paper towel at the bottom and top of the muffins in the container or bag to absorb extra moisture.

If you’d like to freeze them, you can wrap each muffin in a plastic wrap first then put them in a single layer in a freezer-safe bag. They can freeze for up to 3 months. Defrost at room temperature and reheat for about 30 seconds in the microwave and enjoy! 

Recipe FAQs 

Why are my muffins tough and dry?

Tough, dry, and chewy muffins are caused either by overmixing, overbaking, or incorrectly measuring your ingredients (especially dry ingredients). 

Why do you use vegetable oil instead of butter?

Butter evaporates during baking, so I used coconut oil to maintain optimal moisture. If you don’t have coconut oil, you can use a neutral oil like organic canola oil, avocado oil, sunflower oil, or red palm oil to add tenderness and not impact the flavor. 

Do you have to use muffin liners in your muffin tin to make these chocolate muffins?

I recommend muffin liners to keep the muffins from sticking to the pan. If you don’t have them, you use a cooking oil spray to grease your muffin tin instead. 

chocolate chip muffins gf

More recipes to bake at home:

Other Chocolate Chip Desserts to Try

If you tried this Gluten-Free Double Chocolate Muffins or any other recipe on my website, please leave a 🌟 star rating and let me know how you enjoyed it in the📝 comments below. I love hearing from you!

close up of baked chocolate muffins.

How to Make Gluten-Free Double Chocolate Muffins

Gluten-free bakery style chocolate muffins that are filled with melty chocolate chips and come together in one bowl.
5 from 1 vote
Rate Print Save Pin
Course: Breakfast, brunch, Desserts, Snack
Cuisine: American
Diet: Gluten Free
Allergy: Dairy Free, Gluten Free, Vegetarian
Total Time: 35 minutes
Calories: 296kcal
Author: Marina Rizhkov


  • muffin pan
  • bowls
  • spatula
  • measuring spoons


  • cups almond meal, blanched
  • ½ cup organic cocoa, or cacao powder
  • 1 tsp baking soda
  • ½ tsp sea salt
  • 2 pastured eggs
  • cup maple syrup
  • ¼ cup coconut oil
  • 2 tsp vanilla extract
  • ¾ cup mini chocolate chips, or regular chocolate chips


  • Preheat oven to 350°F.
  • Line 12 muffin tins with paper liners.
  • In a medium bowl, mix the dry ingredients (almond meal, cocoa, baking soda, salt) and set aside.
    2½ cups almond meal,, ½ cup organic cocoa,, 1 tsp baking soda, ½ tsp sea salt
    Mixed dry ingredients in a white bowl.
  • In a small pot over medium-low heat, gently melt coconut oil. Whisk in maple syrup. Allow mixture to cool on the stove for a few minutes.
    ¼ cup coconut oil, ⅔ cup maple syrup
    Syrup for gluten free muffins in a white bowl.
  • Next, combine eggs and vanilla extract in a separate bowl. Add coconut oil and maple syrup to the egg mixture and whisk well.
    ½ cup organic cocoa,, 2 pastured eggs, 2 tsp vanilla extract, ⅔ cup maple syrup
    batter for gluten free chocolate muffins in a white bowl.
  • Add the wet ingredients to dry ingredients, mix well, and then fold in the chocolate chips.
    ¾ cup mini chocolate chips,
    gluten free chocolate muffin batter in a white bowl.
  • Fill muffin tins ¾ full.
    batter for chocolate muffins in muffin liners in a muffin pan.
  • Bake for 15-20 minutes or until tops are set (timing depends on the oven, make sure tops are slightly firm before removing from oven).
    Freshly baked chocolate chip muffins in a muffin tin.
  • Allow muffins to cool on a wire rack.
    gluten free chocolate chip muffins on a white board.


  • If you don’t like the taste of coconut oil, it can be replaced with unsalted melted butter.
  • Baking soda can be substituted for baking powder. 


Calories: 296kcal | Carbohydrates: 27g | Protein: 7g | Fat: 20g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 1g | Cholesterol: 29mg | Sodium: 209mg | Potassium: 106mg | Fiber: 4g | Sugar: 19g | Vitamin A: 65IU | Vitamin C: 1mg | Calcium: 90mg | Iron: 2mg
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Recipe Rating


  1. 5 stars
    Thank you for this gluten free recipe. I love muffins too but it’s hard to come by gluten free muffin recipes that aren’t underwhelming. These were perfect!