Healthy Chocolate Muffins with Greek yogurt, applesauce, whole wheat flour, cacao powder, and maple syrup are indulgently fudgy and loaded with chocolate chips! These healthy muffins are a hit with kids, adults, and a guilt free way to satisfy a chocolate craving.

This muffin recipe is a delicious chocolate-y cross between my healthy chocolate bread and healthy chocolate cake. So, if you love one you’ll love them all!

Healthy chocolate muffins in paper liners with mini chocolate chips.

Whole grain healthy chocolate muffins are naturally sweetened plus moist with rich chocolate flavor thanks to yogurt, cocoa powder, and loads of chocolate chips. They’re healthy enough for breakfast but decadent enough for dessert!

Homemade chocolate muffins are better for you than anything store bought and perfect for school lunches, healthy snacks, or baking with your kids. Try healthy apple muffins, too!

Whatever you do, make a double batch and freeze some for later because most of them will be gone within hours!

Why Are Whole Wheat Chocolate Muffins Healthy?

  • No refined sugar (except the chocolate chips!): Naturally sweetened with maple syrup (or honey) and applesauce. Play around with the number of chocolate chips to suit your needs.
  • Protein: The addition of Greek yogurt not only helps with moisture and richness but the bonus is that it provides protein.
  • Whole wheat flour: Less refined than white flour, it’s a more wholesome choice for these muffins!
  • Unsweetened cocoa powder: Cacao powder can also be used, both are loaded with vitamins, antioxidants, and no sugar.
  • These muffins are as good as chocolate zucchini bread, and healthy chocolate ice cream and just as healthy! 

Ingredients for Healthy Chocolate Muffins

  • Eggs: Used for binding and texture but I have even used flax egg. Which acts as a vegan-friendly egg replacer. You could also try chia seed egg for very moist and fudgy results.
  • Applesauce and Greek yogurt: You do need to use both and one cannot be substituted for another. Although applesauce provides a bit of sweetness as is, I opt for unsweetened applesauce to keep it refined sugar free.
  • Maple syrup or honey: Baking is a science and unfortunately you can’t substitute wet sweetener with granulated as it will offset the ratio of liquid: dry ingredients. This means the recipe will not turn out.
  • Cacao or cocoa powder: Use whichever you’d like. From a health standpoint, cacao powder is less processed, but cocoa powder still has a ton of benefits, especially when no sugar is added.
  • Whole wheat flour or spelt flour: Chocolate muffin recipe will not work with any other flour because again “baking is a science”.
  • Baking essentials: Baking powder, baking soda, salt.
  • Chocolate chips: I often use mini chocolate chips so I get a chip in each bite just like with chocolate chip cookies and edible chocolate chip cookie dough, but regular size works too.

Are you a dark chocolate lover? I use semi-sweet chocolate chips because I find they’re the perfect balance of not too sweet, not too bitter but if you prefer dark chocolate, by all means, use dark chocolate chips instead.

whole wheat spelt flour, yogurt, maple syrup, applesauce, eggs and cacao powder

How to Make Chocolate Muffin Recipe

There is a full recipe card below.

  • Prep: Preheat the oven to 325 degrees. Grab a muffin pan and place muffin liners into each cup. Spray with cooking spray (I use Misto). Set it aside.

What to do with the extra batter! You’ll notice a muffin tin holds 12 muffins, but this recipe makes enough for 15. You can either use two tins or bake in batches.

  • Bloom the cacao powder: To a large mixing bowl, whisk boiling water and cacao powder together until well combined. This will help to “bloom” the powder bringing out and maximizing the chocolate flavor.
  • Add the remaining wet ingredients: Whisk in the applesauce and yogurt followed by the eggs and maple syrup. Mix to combine and set aside.
  • Combine dry ingredients: Mix the flour, baking powder, baking soda, and salt. Whisk until smooth and lump-free.
  • Add dry to wet: Slowly add the flour mixture to the chocolate mixture and use a spatula to gently combine.

Allow the batter to sit. Do not overmix! Once the batter has been gently combined, allow it to sit for a few minutes. You will see the chocolate mixture rising and bubbling due to the chemical reaction between the acid in the applesauce and baking soda.

  • Fold in the chocolate chips: Add 1/2 cup and fold them in a few times making sure they’re evenly distributed.
  • Fill and bake: These muffins will rise, so you want to fill each muffin cup to about 2/3 of the way up. Transfer muffins to the oven and place them on the middle rack. Bake for 22 minutes.

The toothpick test. You’ll know your muffins are done when you insert a toothpick into the center and it comes out clean.

  • Remove and let cool: Let your muffins cool in the tin for 5 minutes before placing them on a wire rack to continue cooling completely.

Optional Add-In’s and Variations

  • Dried fruit: Chocolate and cherries are always a great pairing! Cranberries perhaps, or dried mango or coconut.
  • Nuts: Who doesn’t go nuts for chocolate and nuts? Chopped walnuts, pecans, almonds, you name it.
  • Espresso or instant coffee is a great idea! It enhances the chocolate flavor without making anything taste like coffee (although coffee-flavored double chocolate muffins wouldn’t be the worst thing!).
  • Cacao nibs with strawberry jam: Yum! You could use whatever flavor of jam you want.
  • Add a drizzle: Let’s turn this into a triple chocolate muffin! Melt chocolate chips with a bit of coconut oil to melt and then drizzle. Wait for it to set.
  • Added flavor: A dash of cinnamon or a couple of drops of vanilla extract would be delicious especially during the cooler months.

Tips for Best Results

  • For presentation: Reserve a few extra chocolate chips to place on top of the batter just before putting it into the oven. That way when they bake not all of them will be hidden.
  • Allow the batter to rest: Whole wheat flour is a bit denser than regular all-purpose so we want to do everything we can to help these muffins stay nice and light. Allowing the batter to rest (just like pancake batter) gives the leavening agents a chance to activate and create air pockets. If you overmix, you release the air which is what we don’t want.
  • If you plan to freeze some make sure to let them cool completely. 


Can I use all-purpose flour to make these double chocolate muffins?

Absolutely. These muffins will taste just as awesome using all-purpose flour. Whole wheat and all-purpose flour act much the same way you may find the texture to be even softer. You will need to use 1 extra tablespoon of all purpose flour for every cup of whole wheat flour.

Can I use mashed bananas for the applesauce?

Yes! Ripe bananas will provide an incredible sweetness with an element of banana flavor which always pairs well with chocolate (just try banana zucchini muffins with chocolate chips!). It also acts as a binding agent and provides moisture.

Can I make egg free (vegan) chocolate muffins?

Certainly, as long as you use a egg replacer, dairy free chocolate chips, and dairy free yogurt (like coconut yogurt) you’re all set.

Can I make chocolate muffins gluten free?

As I have mentioned in other posts, gluten-free flour can get a little complicated. It’s not always a 1:1 substitution. Your best-case scenario is to use Bob’s Red Mill 1:1 gluten-free flour. I’ve written tips for this in this healthy zucchini muffins post, but other than that I haven’t tried making this chocolate muffin recipe gluten free with anything like almond flour or oat flour. You can make my chocolate coconut flour muffins if you have coconut flour on hand!

When I use gluten free flour I usually have to increase the liquid a bit, so if you do plan to use gluten-free flour just keep in mind there may be some other adjustments you need to make. Let me know if you do try it! 

Chocolate muffins with one unwrapped with a bite missing.

How to Serve Double Chocolate Muffins?

Are they breakfast, snack, or dessert? The answer is all of the above, try them with Greek yogurt frosting for a luscious treat!

How to Store Chocolate Muffin Recipe?

Storing: Muffins stay fresh for up to one week in the fridge. The way these whole wheat chocolate muffins disappear in my house, I always bake a double batch. Always!

Freezing: If you make a double batch (or if you have any leftover muffins), you can always keep them in the freezer. They will last for up to 3 months in an airtight container.

Storage Tip

For more muffin storage practices, check out my posts how to store muffins and how to freeze muffins.

More Healthy Chocolate Recipes

Healthy chocolate muffins with mini chocolate chips in muffin pan.

Healthy Chocolate Muffins

Healthy Chocolate Muffins with Greek yogurt, applesauce, whole wheat flour, cacao powder, and maple syrup are indulgently fudgy and loaded with chocolate chips! They're a hit with kids, adults, and a guilt free way to satisfy a chocolate craving.
4.98 from 35 votes
Servings 15 muffins
Calories 172
Prep Time 10 minutes
Cook Time 22 minutes
Total Time 32 minutes



  • Preheat oven to 325 degrees F, line muffin tin with liners and spray inside with cooking spray (this recipe makes 15 muffins or so, so either bake in 2 tins or 2 batches). Set aside.
  • In a large mixing bowl, add cacao powder and boiling water; whisk until well combined. This step will bloom the cacao powder and make muffins more flavorful. Add applesauce and yogurt; whisk. Now add eggs and maple syrup; whisk until smooth. Set aside.
  • In a medium mixing bowl, combine flour, baking powder, baking soda and salt. Whisk until no lumps, add to the bowl with chocolate mixture and gently mix with a spatula just enough to combine. Do not over mix, let batter sit for a few minutes, then stir again. Add 1/2 cup chocolate chips and give a few gentle stirs to incorporate.
  • Fill each opening 2/3 batter full and sprinkle chocolate chips on top (this recipe makes 15 muffins or so, so either bake in 2 tins or 2 batches). Bake on a middle rack for 22 minutes or until a toothpick inserted in the centre comes out clean.
  • Remove from the oven, let muffins cool for about 5 minutes and transfer to a cooling rack to cool off a bit more and then enjoy!


  • Store: In a cool dry place covered for 2 days, then refrigerate in an airtight container for up to 3 more days.
  • Freeze: In an airtight container up to 3 months.
  • Applesauce and Greek yogurt: You do need to use both and one cannot be substituted for another. 
  • Maple syrup or honey: Baking is a science and unfortunately you can’t substitute wet sweetener with powdered as it will offset liquid:dry ingredients ratio and recipe will not turn out.
  • Whole wheat flour or spelt flour: Chocolate muffin recipe will not work with any other flour because again “baking is a science”.
  • Egg replacement: Flax egg or try chia seed egg.
  • Why boiling water? Hot liquid helps to bloom the cacao powder making the chocolate muffins more flavorful. 
  • Cacao powder: Cacao powder is less processed and more nutritious than cocoa powder. But both will work.
See recipe post for more tips and FAQs.


Serving: 1muffin | Calories: 172kcal | Carbohydrates: 33g | Protein: 5g | Fat: 4g | Saturated Fat: 3g | Trans Fat: 1g | Cholesterol: 22mg | Sodium: 190mg | Fiber: 3g | Sugar: 18g
Course: Dessert
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. I haven’t made these yet but several people mentioned “drizzle” in their reviews and I can’t find the directions for it in the recipe! I’m VERY interested and have spent a long time looking for these directions, through other muffin recipes, etc and simply can NOT find them! Please put them somewhere easy to find as I’m just crazy to try this recipe WITH the drizzle! Thank you so much and I just love all your recipes!

    1. Sorry made you look that long. 🙂 It used to be on older recipe. All it is just melted chocolate chips with a bit of coconut oil to melt and then drizzle and it will set.

    1. You might. I have not tried though. General recommendation is to use 1 cup of white flour for every 3/4 cup of whole wheat flour that recipe calls for.

  2. 5 stars
    Another great keeper recipe, simply awesome. I replaced half cup of whole wheat flour with almond flour and added some finely chopped walnuts along with the chocolate chips and didn’t add the 2tbsp maple syrup. The muffin turned out pillowy soft and mildly sweet just like the way we like it in our home. And I totally agree with you on how the north American kids’s diet is out of control and loaded with sugar. With our authority as a parent we can definitely change that. Anyway thanks for the great recipe.

  3. 5 stars
    Hi! Olena!
    Would substituting mashed bananas instead of applesauce be ok?
    Looking forward to another delicious creation! (I need to use up my ripe bananas. )

      1. Tried them already and I’m in loooove ? my sister and I just made two batches today as well.

        However, my brother is a huge fan of banana flavor… any advice on how to make the banana flavor more intense ?

        1. Add banana extract.:) Maybe there is a natural one! Or add crushed banana chips, they are already flavored.

  4. 5 stars
    This was a great recipe. I have been trying out different chocolate muffin recipes and this is the best I have tried. Only change I made was using flax eggs instead of regular.

  5. 5 stars
    Another delicious recipe Olena. I find I usually end up back on your website when I want something sweet and healthy that is straightforward to make. I only had raw cacao nibs on hand which are kind of bitter so added a couple of tablespoons of homemade strawberry jam to compensate. Delicious!

    1. Yay! So happy to hear my healthy chocolate muffins were a hit with you. Smart move – you must have Ukrainian in you! No need to waste gas and time on store trips, right?! Yes, cacao nibs are bitter.

4.98 from 35 votes (4 ratings without comment)

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