Healthy Chocolate Muffins {Gluten Free and Dairy Free}

Rich and decadent healthy chocolate muffins made gluten free and dairy free. These naturally sweetened muffins are made with coconut sugar and stevia sweetened chocolate.

Healthy chocolate muffins. The best gluten free breakfast.

I really loved using the Lily’s Intense Dark Chocolate because it’s sugar free and the dark chocolate is vegan.

Lily’s has seriously been one of my favorite chocolate brands. The brand has been around since the 1970’s and they make sure that their products are harvested through Fair Trade Practices and are botanically sweetened.

You can’t tell the difference between them and their refined sugar equivalent. That means that your baking is still going to be so chocolatey. There are so many vegan chocolate options with the Lily products.

What you need to make these healthy chocolate muffins

I baked these delicious gluten free muffins as a healthier alternative when I’m having a hankering for chocolate cake.

These muffins are sweetened naturally using coconut sugar and made using a blend of gluten free flours. You are going to love these muffins!

  • eggs
  • coconut sugar
  • coconut oil, melted
  • applesauce, unsweetened
  • vanilla extract
  • oat milk or plant milk
  • gluten free baking flour (all purpose)
  • tapioca flour or arrowroot flour
  • almond flour
  • unsweetened cocoa powder
  • baking soda
  • baking powder
  • salt
  • Lily’s Chocolate


For the eggs, you can use an egg replacer to make these vegan.

If you don’t want to use applesauce, you can use mashed banana.

For the coconut oil, you can use melted dairy free butter or canola oil.

Healthy chocolate muffins. The best gluten free breakfast.

can’t get enough gluten free desserts? 

I hear ya! These cashew butter cookies are quickly becoming one of my favorites and if you like this recipe than you will love these gluten free dessert recipes:

SunButter Chocolate Chip Cookies

Triple Chocolate Gluten Free and Dairy Free Cupcakes

Gluten Free and Dairy Free Raspberry Pop Tarts

Here is the complete list of healthy dessert recipes on this site – enjoy!

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Healthy chocolate muffins. The best gluten free breakfast.

If you are still reading this far, you definitely deserve some healthy chocolate muffins and if you make this recipe or any other recipe from the blog, be sure to tag @peanutbutterpluschocolate on Instagram and check me out on Facebook and Pinterest!

Also, don’t forget to leave me a comment after the recipe card at the bottom. I really love chatting with all of you, hearing about how your recipe turned out and answering any questions you have.

Happy Baking!

Healthy Double Chocolate Muffins

The best healthy double chocolate muffins made refined sugar free, gluten free and dairy free.
Pin Recipe
Prep Time10 minutes
Cook Time18 minutes
Total Time28 minutes
Course: Breakfast, Dessert
Keyword: chocolate muffin, refined sugar free
Servings: 12
Author: Ciarra Siller


  • 2 eggs room temperature
  • 1/2 cup coconut sugar
  • 1/3 cup coconut oil melted
  • 1/2 cup unsweetened applesauce
  • 1/3 cup oat milk or plant milk
  • 2 tsp vanilla extract
  • 3/4 cup gluten free baking flour all purpose
  • 1/2 cup almond flour
  • 1/4 cup tapioca flour
  • 1/2 cup unsweetened cocoa powder
  • 1 1/2 tsp baking powder
  • 1 tsp baking soda
  • 1/4 tsp sea salt
  • 2 Lily's Dark Chocolate Bars chopped


  • Preheat the oven to 350 F and prepare a muffin tin with liners and then set it aside.
    Place the eggs, coconut sugar, applesauce, almond milk and vanilla into a mixing bowl and beat using a whisk until smooth. Add in the remaining dry ingredients (except the chopped chocolate) and stir until no dry spots remain and batter forms.
  • Fold in the chocolate pieces and use a cookie scooper and or ice cream scooper to fill the liners about 3/4 of the way. Bake the muffins for 18-20 minutes.
  • Let cool before serving. Store the muffins in an airtight container for up to 3 days.


If you have any questions or want to tell me about how this recipe turned out, don’t hesitate to leave me a comment below this recipe card at the bottom! I love hearing from you!
Amazing dairy free chocolate

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I'm Ciarra

Welcome to Peanut Butter Plus Chocolate, where I share indulgent dessert recipes. Here you can find healthier versions of your favorite desserts.



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