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Recipe for Chocolate Chip Muffins

Recipe for Chocolate Chip Muffins – Chocolate fans unite together for this amazingly decadent double chocolate recipe for Chocolate Chip Muffins.

With a creamy chocolate spread. And yes, I did say muffins — so bake up a tray of these for an easy make-ahead breakfast. But trust me, they will not last long.

recipe for chocolate chip muffins

If Muffins Wars Existed… This Recipe for Chocolate Chip Muffins Would Win!

As far as I can tell, the gourmet cupcake craze is still in full swing. What then can a clean eating enthusiast substitute for a cupcake?

Yep, you guessed it… muffins! And trust me, the recipe for chocolate chip muffins below can totally hold its own in the cupcake wars. Once you add the Recipe for Chocolate Spread, the war is won (wink).

recipe for chocolate chip muffins

What is the difference between Chocolate Chip Cupcakes and this Recipe for Chocolate Chip Muffins?

Oh there’s a big difference, people! I decided to Google Chocolate Chip Cupcake and the first recipe that popped up had the following ingredients on their recipe card:

  • Cake flour
  • Butter
  • Refined White Sugar
  • Milk
  • Semi-sweet chocolate chips

YIKES! This is a whole lot of unhealthy that makes cupcakes definitely not even close to healthy. Unless of course, you try to make this Recipe for Lemon Cupcakes using cassava flour too!

recipe for chocolate chip muffins

Just do a Quick Comparison with our Recipe for Chocolate Chip Muffins:

Compare the above standard chocolate chip cupcake ingredients with the ingredients I use for this recipe for chocolate chip muffins. Plus, of course, we used the baking powder, pure vanilla extract, sea salt and eggs… but we used pastured ones instead.

Here are the 7 changes I made to ensure this recipe was absolutely delicious and ready to enjoy by all.

#1: Cassava Flour is the Best Thing Since Gluten Free Flour

Cassava flour is a great ingredient to swap with conventional whole grain flours such as whole wheat or spelt flour. Plus, it’s naturally gluten free.

In many recipes it can be substituted in a 1:1 ratio for whole wheat flour. It’s also a great source of vitamin C (1/4 cup has almost 20% of your Daily Value), folate, magnesium, potassium and many additional nutrients.

We have started to use cassava flour more here at Clean Cuisine. So, if you buy yourself a bag of our favorite brand Otto’s Cassava Flour, be sure to visit these top recipes.

#2: Raw Cacao Powder for the best Superfood Chocolatey Boost

A known superfood, raw cacao powder contains a hefty dose of two nutrients most people need more of: magnesium and iron. Plus, cacao powder is rich in phytonutrients, fiber and antioxidants.

#3: Sweeten this Recipe for Chocolate Chip Muffins Naturally

Believe it or not, succulent sweet maple syrup is actually not an empty calorie sweetener. Derived from the maple tree, real and unrefined maple syrup has phytonutrients and disease-fighting antioxidants, including polyphenols.

#4: Oh, We Just Love Mashed Bananas in our Recipes

Thanks to their high percentage of a special “miracle fiber”, bananas are an excellent food for weight management. Bananas are also a delicious source of prebiotics, potassium, fiber, vitamin C and vitamin B6. Packing a powerfully sweet nutritional punch, bananas not only sweeten this recipe for chocolate chip muffins. But, they also contribute a lovely moist texture too.

#5: Load Up this Recipe with Omega-3’s Using Chia Seeds

Chia seeds are a super easy food for any health-conscious baker to love. Chia seeds not only contribute an omega-3 and fiber boost to this recipe for chocolate chip muffins, but they also improve their texture.

#6: Swap Cheap Eggs for Pastured Eggs

There is a BIG difference between conventional eggs used in your typical cupcake recipe and the pastured eggs I use in this recipe. Be sure to read the health benefits of eating eggs raised on pasture.

#7: All About the Chocolate Chips – Dairy Free, of course!

Since every other component of this recipe for chocolate chip muffins is healthy, you can go ahead and use regular chocolate chips if you want. However, we still will recommend dairy-free dark chocolate chips from Enjoy Life because they are so delicious.

However, if you’re looking to keep this recipe super clean — cacao nibs are the superfood choice as they have the same impressive nutrition and antioxidant profile of cacao powder.

recipe for chocolate chip muffins

Last but Not Least – Recipe for Chocolate Spread

If you love chocolate as much as my children — then make this recipe for Chocolate Chip Muffins a triple chocolate threat. Cacao Muffins with my Recipe for Chocolate Spread and topped with mini Enjoy Life Chocolate Chips.

With just 5 simple ingredients, you can make the chocolately frosting as thin or as thick as you want. So, there might be one ingredient that’s not a staple in your kitchen, like it is in mine. Pecan Butter.

recipe for chocolate chip muffins

I am working on a pecan butter recipe — so stay tuned.

But quickly note the following:

  1. Just toss about 2 cups of raw pecans in the oven on 300 for about 6 minutes OR in a small skillet on the stovetop until they begin to sweat, about 3-5 minutes.
  2. Let them cool completely and add them to a food processor for several minutes, scraping the sides as you go. Add in a little sea salt — and cinnamon if you like.

Then, go make this Recipe for Chocolate Spread and these delicious chocolatey breakfast muffins.


Recipe for Chocolate Chip Muffins

Recipe for Chocolate Chip Muffins – the perfect breakfast for chocolate lovers. Loaded with nutrients and delicious, make a double batch.

recipe for chocolate chip muffins
Save Recipe
  • Prep Time: 15 minutes
  • Cook Time: 18 minutes
  • Total Time: 33 minutes
  • Yield: 1218 1x


  • 1 1/8 cups cassava flour (or 1 1/2 cup gluten free flour)
  • 1/3 cup cacao powder
  • 1/4 cup chia seeds
  • 1 teaspoon baking soda
  • 1/2 teaspoon sea salt
  • 1 1/4  cup almond milk
  • 1 cup plus pure maple syrup
  • 1/2 cup banana, mashed
  • 1 teaspoon lemon juice
  • 1/2 teaspoon pure vanilla extract
  • 3 pastured egg whites
  • 1 cup dairy-free dark chocolate chips
  • 1 batch of Chocolate Spread


  1. Preheat oven to 350 degrees. Line 12-18 muffin cups with paper liners.
  2. In a large bowl, mix together the flour, cacao powder, chia seeds, baking soda, and sea salt.
  3. In a classic batter bowl, mix together the almond milk, maple syrup, banana, lemon juice and vanilla extract with a handmixer until creamy.
  4. Add the wet ingredients to the dry ingredients on low with the handmixer or a wooden spoon. Stir until well combined.
  5. In another classic batter bowl, beat the 3 egg whites to stiff peaks. Carefully fold the egg whites into the batter. Fold in the chocolate chips and scoop into the muffin liners.
  6. Bake for 18 to 22 minutes or until a toothpick inserted in the middle comes clean. Set on a wire rack to cool. While baking, prepare a batch of our delicious Chocolate Spread
  7. Serve warm or room temperature.

Last Step! If you loved our recipe, leave us a review below. This helps future recipe makers and ensures continued high-quality recipes for years to come!


Chocolate Chip Muffins can be stored in the fridge for up to 4 days or in a zip-top bag in the freezer for up to 3 weeks.

© 2024 clean cuisine Recipe by:

Aimee Niedosik

Aimee loves to craft delicious, nutrient-dense recipes to share with her family and friends. While in remission from autoimmune diseases and underlying viruses, she still maintains an anti-inflammatory and anti-aging diet. Aimee is a Christian, website designer, autoimmune community leader and lives in North Carolina with her husband, 2 kids and 2 dogs.

recipe for chocolate spread
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