Clean Eating Chocolate Coconut Muffins

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Bite into something moist and chocolatey - without the guilt!

Sugar gets a bad rap, and it’s true that added sugars aren’t usually part of a healthy diet. But, these sweet and cakey Clean Eating Chocolate Coconut Muffins can be an exception. They manage to appease your sweet tooth while keeping your energy levels stable and your sugar addiction firmly at bay.

It’s easy to scan a recipe’s nutritional information and be scared off by 5 grams of sugar. However, refined white sugar is the most processed form of sucrose you can choose. Swapping it out for less processed sugars like honey, maple syrup, or coconut sugar (which we use in this recipe) is a way to improve your overall health. That’s not to mention the extra flavor and aroma they add! We love any desserts that sneak in healthier ingredients while tricking our taste buds. With recipes like this (and other favorites, like Chocolate Chip Pumpkin Bread or Zucchini Bread), your guests will never know you’re serving them healthy desserts!

Chocolate Coconut Muffins Aren’t Just for Dessert

This recipe makes an excellent breakfast or pre-workout choice. Oats are a high-fiber, high-protein base for these indulgent muffins. They give you the calorie input you need to maintain high energy levels. Add in Greek yogurt’s protein content, which aids muscle growth and repair, you’ll be feeling good all day long.

We’ve all read about the health benefits of coconut oil. It may reduce abdominal fat, increase good HDL cholesterol, and reduce appetite. We could go on! But this recipe doesn’t just stop at coconut oil. Coconut flakes and sugar also boost these muffin’s fatty acid power-up. One disclaimer, though: It’s best to be picky when buying store-bought applesauce. Cheaper brands are often loaded with added sugar. If you have time, make your own slow cooker applesauce from the comfort of your own kitchen.

Making This Recipe Plant-Based and Gluten-Free

For our vegan friends out there, you can choose non-dairy chocolate chips (like Enjoy Life) and dairy-free yogurt to make this a plant-based recipe. This recipe can also easily be made gluten-free by buying certified gluten-free oats.

Either way, this clean-eating muffin recipe is sure to head to the top of your favorites list! If you’re not a chocolate fan (gasp!), you can easily add chopped fruits or nuts instead. My personal recommendation would be pear. You could also add pistachios or dried bananas – anything that tickles your fancy, really. It’s actually a great recipe for using up old pantry ingredients. Yes, that’s what we like to hear!

As a bonus, this recipe only takes 15 to 18 minutes in the oven. These coconut chocolate delights are a great treat to bring along to picnics or hikes. If that doesn’t win the hearts of your friends, I don’t know what will.

Check out these other 101 Uses for Coconut Oil.

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Clean Eating Chocolate Coconut Muffins

By using less processed sugar and natural ingredients, this muffin recipe is a clean eating sweet treat you don't have to feel guilty about.
Prep Time 10 minutes
Cook Time 18 minutes
Total Time 28 minutes
Yield 12 people
Serving Size 1 muffin
Course Dessert
Cuisine Universal
Author SkinnyMs.


  • 1 3/4 cup rolled oats
  • 3 tablespoons coconut oil unrefined
  • 1/2 cup applesauce unsweetened
  • 1/2 cup cocoa powder unsweetened
  • 1/2 cup coconut palm sugar
  • 1 tablespoon pure vanilla extract
  • 1/2 cup Greek yogurt plain
  • 1/2 teaspoon cream of tartar
  • 1 1/2 teaspoon baking powder
  • 1 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 cup hot water
  • 1/2 cup chocolate chips for gluten-free use Enjoy Life brand
  • 1/4 cup coconut flakes unsweetened


  • Preheat oven to 350 degrees. Line a muffin pan with 12 cupcake liners.
  • Put all ingredients except the chocolate chips and coconut flakes in a high powered blender or food processor. Blend until well combined and oats are ground. Stir in chocolate chips by hand.
  • Pour batter evenly in the cupcake liners. Sprinkle with coconut flakes. Bake for 15-18 minutes, until a toothpick inserted in the center comes out clean. Cool completely.

Nutrition Information

Serving: 1muffin | Calories: 199kcal | Carbohydrates: 26g | Protein: 6g | Fat: 10g | Saturated Fat: 6g | Cholesterol: 1mg | Sodium: 224mg | Fiber: 5g | Sugar: 5g |
SmartPoints (Freestyle): 8
Keywords Gluten-Free, Kid-Friendly, Quick and Easy, Vegetarian

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The SkinnyMs. team believes that all people, regardless of age, size, and fitness level, have the power to transform their lives — they just need the resources to do so. The SkinnyMs. method promotes healthy living through a combination of clean eating and regular exercise. We offer everything you need to be successful.

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  1. I just made these to send in the kids' lunches for dessert. They loved them! I was wondering, do you store these in the refrigerator?

    1. We use organic, virgin coconut oil that is unrefined. If you have a Trader Joe’s nearby, they sell a very affordable jar that fits the bill. 🙂

    1. Sheri, We haven’t tried this recipe with coconut flour so I can’t say for certain. This info I located regarding substituting with coconut flour when baking:

      In baking, you cannot substitute coconut flour for wheat or other grain-based flours at a 1:1 ratio. … In baked goods, you generally want to substitute 1/4 cup to 1/3 cup coconut flour for 1 cup grain-based flour. You will also need to increase the number of eggs.

  2. I bake a lot and didn’t find this recipe to be great. I love the idea of healthy chocolate coconut muffins but felt like this recipe needs some tweaking. Is it missing eggs (or egg substitutes) maybe?

    My muffins took much longer to bake than the posted time and the insides were still a little gooey when the outsides were getting dry and crumbly. The texture of the finished product was a little off, but the flavour was good 🙂

    1. Desiree, Not all muffins have eggs. This is one of my favorite muffin recipes and it’s plant-based, no eggs or dairy.
      Also, it’s very chocolatey. Sometimes I’ll use only 1/3 cup vs 1/2.

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