Healthy Chocolate Chip Muffins Recipe

This healthy chocolate chip muffins recipe makes a delicious, whole grain treat after dinner or on the go!

There’s just something about healthy chocolate chip muffins. I bite into their soft, spongy little bodies, and I’m immediately whisked away to my fabulously warm and sweet-scented dream kitchen and that perfect, double oven I keep fantasizing about. My stress seems to melt away and the only thing occupying my mind is that deep, rich gooey chocolate that seems to massage my shoulders and rub my feet on the way down.

A healthy chocolate chip muffin sits broken open showing off all its inner chocolatey chips.


Typically, a muffin is heartier. It’s often made with whole grains and is also often filled with healthier fare such as dried fruits, nuts and seeds. Muffins can be sweet or savory. They can sometimes be very similar to cupcakes, however, but cupcakes are basically tiny cakes. So there is a difference.


That is the broadly held idea. However, it’s not always the case. A muffin can be made just as sugary and just as unhealthy as a cupcake. While a cupcake is definitely cake in a smaller form, a muffin can have just as much refined sugar, process grains and other additives that many cupcakes have. And on the other side of that, a cupcake can be made with whole grains and healthier ingredients. So it all really depends on what you put into your muffins and cupcakes.

All that being said, these muffins, despite containing honey and chocolate chips, are a pretty good way to go if you are craving something sweet. They are unprocessed, whole grain muffins that use healthier ingredients at every turn. You can’t go wrong!

One of these Clean Eating Chocolate Chip Muffins is broken open to show off the lovely, chocolate chip filled center.


If you are wanting a good  base recipe to use for other muffins, this is a great one. Sub the chocolate chips with other things like berries, dried fruits, nuts, seeds, whatever you can think of that fits into your definition of health and clean!


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Clean Eating Chocolate Chip Muffins

Healthy Chocolate Chip Muffins

A delicious snack or dessert that everyone will love!
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Course: Dessert, Muffins, Snack
Cuisine: American
Prep Time: 15 minutes
Cook Time: 30 minutes
Total Time: 45 minutes
Servings: 24 muffins
Calories: 125kcal


  • 2 cups whole wheat pastry flour (affiliate link)
  • 2 tsp. baking soda
  • 1 large egg
  • ½ cup honey
  • ¼ cup oil (anything light in flavor)
  • ¾ cup milk (I used unsweetened almond milk)
  • 2 tsp. ground cinnamon
  • ½ cup unsweetened apple sauce
  • 1 cup chocolate chips (either grain sweetened, low carb or dark chocolate are the cleanest choices)


  • Preheat oven to 350 degrees F.
  • Line your muffin tin with cupcake papers.
  • In a medium mixing bowl, whisk together the flour, chocolate chips and baking soda.
  • In a large mixing bowl, blend everything else with a whisk.
  • Add the flour to the wet ingredients and whisk again.
  • Pour into your muffin tin. Fill up the cups only half way.
  • Bake for 20 minutes or until a toothpick poked in the middle of a muffin comes out clean.


Please note that the nutrition data given here is a ballpark figure. Exact data is not possible.


Serving: 1muffin | Calories: 125kcal | Carbohydrates: 19g | Protein: 2g | Fat: 5g | Saturated Fat: 2g | Cholesterol: 11mg | Sodium: 125mg | Potassium: 59mg | Fiber: 2g | Sugar: 11g | Vitamin A: 40IU | Vitamin C: 0.2mg | Calcium: 27mg | Iron: 0.6mg
Recipe from the Gracious Pantry archives, originally posted 12/31/10.

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  1. just pulled these out of the oven a short while ago, and they are amazing!! swapped the apple & oil for fresh butter, but my little boy will wolf these down as a lunch box treat!! 😉

    1. The Gracious Pantry says:

      Awesome! Glad you’re enjoying them! 🙂

  2. Do you think it will mess up the muffin if i use regular flour and semi sweet chocolate chips?

    1. The Gracious Pantry says:

      Lynn – In theory, it should be fine.

  3. Can I substitute gluten free flour or coconut flour?

    1. The Gracious Pantry says:

      Allison – Technically, but you’ll probably need more of it to achieve the same consistency. Coconut flour is very “thirsty” stuff.

  4. Ok, thanks for the response!!!