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!
Table of contents
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.
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.
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.
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.
Certainly, as long as you use a egg replacer, dairy free chocolate chips, and dairy free yogurt (like coconut yogurt) you’re all set.
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!
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!
- For breakfast: Muffins are a great grab ‘n go breakfast for busy mornings but a basket of fresh healthy muffins is also nice to have on your brunch table. Serve along with a loaf of healthy chocolate bread, healthy waffles, or overnight oats and you’ve got a Sunday morning feast or holiday brunch with something for everyone!
- As a snack: Whether a pick-me-up in the afternoon with a cup of tea, an afterschool snack for the kids, or a healthy recess snack for school these muffins are always a hit. Healthy chocolate chip muffins, healthy chocolate chip cookies, and banana protein muffins are some other ideas!
- Enjoy as a dessert: These muffins are as decadent as any cupcake so why not enjoy it like one! Top with a healthy chocolate frosting, or a chocolate drizzle and serve with an array of other desserts like these healthy vanilla cupcakes with a buttercream frosting.
- Wash them down with a mug of healthy hot chocolate or a delicious green smoothie. Healthy iced coffee is a real treat in the summer!
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.
More Healthy Chocolate Recipes
Healthy Chocolate Muffins
- 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
- 2 tsp baking powder aluminum free
- 1 tsp baking soda
- 1/4 tsp salt
- 1 3/4 cups + 3 tbsp whole wheat or spelt flour
- 3/4 cup chocolate chips divided
- Cooking spray I use Misto
- 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.
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!
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. You can check out my tips on healthy zucchini muffins. Also 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!) 🙂
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!
Hi we love these choc muffins.Thank you for the recipe.
You’re welcome June!
These were deliciously fudgy and moist!