These Healthy Chocolate Muffins are indulgently fudgy, fluffy and moist. Made with whole grains, no oil, naturally sweetened and loaded with chocolate chips.
Reader’s Review
I made these muffins for the 1st time at weekend, oh boy! What a hit they were too, so soft, moist and so tasty! Will definitely be a regular bake in this house.
Julie
Why You’ll Love These Muffins
I used the batter from these healthy chocolate muffins to make Dubai chocolate muffins and was instantly reminded how good they are! And then I read the comments and I see you guys are in love with them too!
They taste so indulgent but in fact are a true definition of a healthy muffin! No oil, refined sugar (except in the chocolate chips), naturally sweetened with maple syrup, and moistened with yogurt and applesauce.
The addition of Greek yogurt not only helps with moisture but the bonus is that it provides protein. I use whole wheat flour or spelt flour which is a more wholesome choice for this healthy chocolate muffin recipe!
Ingredients for Healthy Chocolate Muffins
- Cacao or cocoa powder: Use whichever you’d like. From a health standpoint, cacao powder is less processed, but unsweetened cocoa powder still has a ton of benefits.
- Whole wheat flour: I like to use whole wheat flour or spelt flour. I think white whole wheat flour or whole wheat pastry flour will work 1:1 ratio.
- Applesauce and 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. Greek or regular yogurt works.
- Eggs: Used for binding and texture.
- Maple syrup: You can use any other liquid sweetener you like. Examples would be honey, agave, sugar-free syrup etc.
- Baking essentials: Baking powder, baking soda and salt.
- Chocolate chips: I often use mini chocolate chips so I get more chocolate in each bite but regular size works too. 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.
Substitutions
- All-purpose flour: I do have a conversion chart that I often use in baking. I have not tried all-purpose flour in this specific chocolate muffin recipe but if I were to, I would use 2 1/4 cups of all-purpose flour.
- Gluten-free flour: 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 gluten-free baking blend and use above mentioned 2 1/4 cups white flour sub measurements. I haven’t tried oat flour or almond flour.
- Mashed banana instead of applesauce: Ripe bananas will provide an incredible sweetness with an element of banana flavor which always pairs well with chocolate. Use same amount as applesauce.
- Egg-free: You can try an egg replacer or flax eggs or chia eggs.
How to Make Healthy Chocolate Muffins
A muffin tin holds 12 muffins but this recipe makes enough batter for 15 muffins. You can either use 2 muffin pans or bake in batches.
Preheat 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.
- “Bloom” the cacao powder: In a large mixing bowl, whisk boiling water and cacao powder. This will help to gain that rich chocolate flavor.
- Add 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 ingredients: Add the flour mixture to the chocolate mixture, stir gently and let batter sit for a minute, then stir again. Do not overmix.
- Add chocolate chips: Add 1/2 cup of chocolate chips and fold them in a few times making sure they’re evenly distributed.
- Bake and cool: Fill each muffin opening 2/3 full with batter and sprinkle with remaining 1/4 cup of chocolate chips. Bake on a middle rack for 22 minutes. You’ll know your muffins are done when you insert a toothpick into the center and it comes out clean. Let your muffins cool in the tin for 5 minutes before placing on a wire rack to continue cooling.
Additions and Variations
- Dried fruit: Chocolate and cherries are always a great pairing! Add up to 1/2 cup. Cranberries perhaps, or dried mango or coconut.
- Nuts: Add up to 1/3 cup of chopped walnuts, pistachios, pecans, almonds, you name it.
- Espresso or instant coffee: It enhances the chocolate flavor without making anything taste like coffee.
- 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, then drizzle on top and wait for it to set.
- Added flavor: A dash of cinnamon or a couple drops of vanilla extract would be delicious especially during the cooler months.
How to Store
Store: Healthy chocolate muffins stay fresh for up to 3-4 days in a cool dry place. The way these muffins disappear in my house, I always bake a double batch. Always!
Freeze: 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
- Chocolate veggie muffins
- Healthy chocolate zucchini bread
- Healthy chocolate chip muffins
- Chocolate coconut flour muffins
- Chocolate quinoa muffins
- Chocolate zucchini muffins
- Healthy chocolate bread
Healthy Chocolate Muffins
Equipment
Ingredients
- 1/2 cup cacao or cocoa powder
- 1/2 cup boiling water
- 3/4 cup applesauce, unsweetened
- 1/2 cup plain Greek or regular yogurt, 2%+ fat
- 2 large eggs
- 3/4 cup maple syrup or honey
- 1 1/2 teaspoons baking powder, aluminum free
- 1 teaspoon baking soda
- 1/4 teaspoon salt
- 1 3/4 cups+ 3 tablespoons whole wheat or spelt flour
- 3/4 cup chocolate chips, divided
- Cooking spray, I use Misto
Instructions
- Preheat oven to 325 degrees F, line muffin tin with liners and spray with cooking spray. This recipe makes 15 muffins or so, so either bake in 2 tins or 2 batches. Set aside.
- In a large bowl, add cacao powder and boiling water; whisk until smooth. Add applesauce and yogurt; whisk. Now add eggs and maple syrup; whisk until smooth. Set aside.
- In a medium 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 remaining 1/4 cup of 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.
Notes
- Store: In a cool dry place covered for 3-4 days.
- Freeze: In an airtight container up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
I was making these with cocoa powder and they were great. I love dark chocolate and decided to try dark chocolate cocoa powder. They were amazing!
I’m so happy to hear that, Linda!
I have made these several times. This recipe always comes out perfect. It’s my go to when I’m craving a healthy chocolate treat. 🙂 Thanks for another keeper!
I’m so happy to hear that, Olya!❤️
I make a cake with the this recipe and not muffins and I use light sour cream in place of the yogurt and the it came out moist and tasty.very delicious yum 😋😋
I’m so happy to hear this! Sour cream cakes are the best! I love tangy sour cream taste in a cake!
Incredibly delicious! I used Icelandic Skyr Yogurt 0% fat to add more protein and less fat. The muffins turned out moist chocolaty.
I’m so glad you enjoyed these healthy chocolate muffins! Thank you for the wonderful review!
These muffins are so awesome. I have made the recipe multiple times and everyone who eats them asks for me to make them again. Thanks.
I’m so happy to read this! Thanks for your positive feedback!
Wow!!
I tweaked mine though..
I used Paleo flour instead and added some chocolate plant protein powder with some no sugar sweetener powder too ontop of the other ingredients as stated.
I also used sugar free chocolate chips!
Wow! To think I only use one point on 5 mini donuts (what I made them into)
Thanks for the recipe!
Thanks for letting us know how you made it, glad it turned out so well for you!
These have such a delicious flavour! I used GF plain four, and they turned out sticky and stretchy inside. Is there a trick to substituting GF flour for whole wheat flour?
They were delicious aside from the texture, which is clearly my mistake!
Hmmm. I haven’t baked with GF flour a lot but whatever I tried in muffins I noticed to add a bit more liquid. I heard Bob’s Red Mill is the best 1:1 substitute. Hope this helps.
these are amazing!! love them so much!!! 🙂
Yay! So happy to hear!
Hi! I can’t wait to try these! I only have metal muffin tins, not silicone… Will that be a problem? (I’m new to baking!) 🙂
~Morgan
No problem at all. Spray it well with cooking spray or use parchment paper liners sprayed with cooking spray. Enjoy!
I messed up at added too much baking soda. So I doubled the batch – so glad I did! These are amazing. I don’t know if my double batch will make it to the freezer. Another amazing recipe.
Haha, these are very very good as per my kids. I’m so glad you enjoyed it, Melissa! Thank you for the wonderful review!