On the morning of one of our big baseball trips, my dad and I arrived at the airport early. With our itinerary safely tucked inside of a folder in my backpack, the schedule of MLB stadiums and game tickets nestled behind hotel and rental car reservations, plus enough sightseeing suggestions and maps to cover the entire Midwest, we rolled our carry-on suitcases through the terminal to our departing flight’s gate.
After finding two seats in the waiting area, I watched our luggage while my dad headed towards the nearest coffee shop. We left the house before he could finish his usual large home-brewed pot, but before he walked away to join the queue of tired-looking travelers, he asked if he could get anything for me.
“Just water!” I chirped, remembering the homemade breakfast bars stashed inside of my backpack.
He returned a while later, holding a tall steaming mug in one hand and a paper bag in the other. He pulled out two gigantic water bottles first, handed one to me and tucked the other into the mesh side pocket of his own backpack, then reached back into the bag.
This time, he produced a smaller brown paper bag, one simply folded over at the top. It held a single chocolate muffin, deep brown with plenty of chocolate chips studding its top, and after peeling back the white paper wrapper around its sides, my dad offered me a bite.
I broke off a tiny piece and popped it into my mouth. Supremely rich with an almost cupcake-like chocolate flavor, plenty of oil gave it an incredibly moist texture, and even more chocolate chips hid inside. Although completely delicious, it tasted like dessert trying to masquerade as breakfast… And knowing the usual ingredients of bakery-style muffins, I knew that probably wasn’t too far from the truth.
But now, far too many years later, I finally perfected a healthy homemade version: these ultimate healthy chocolate muffins! With two different types in the batter, they’re a chocolate lover’s dream – and unlike those coffee shop ones, these double chocolate muffins are made with more wholesome ingredients… And definitely healthy enough for breakfast!
QUICK OVERVIEW – THE ULTIMATE HEALTHY CHOCOLATE MUFFINS
Difficulty: Fairly easy, including for many beginner bakers.
Taste: A chocolate lover’s dream! Very rich and decadent with a prominent chocolate flavor (similar to 72-75% dark chocolate!) filling every bite.
Texture: Really moist, on the denser side, and almost fudgy like brownies; then studded with smooth chocolate morsels on top and throughout that melt in your mouth.
KEY INGREDIENTS TO MAKE THE ULTIMATE HEALTHY CHOCOLATE MUFFINS
Let’s go over the ingredients you’ll need to make these healthy chocolate muffins! I’m assuming you already have baking staples like salt, vanilla, and milk, so we’ll focus on the more interesting and important ones here.
Unsweetened cocoa powder. This is the first chocolate component in these double chocolate muffins! You’ll actually use just as much cocoa powder as flour (more on that in a moment!), which gives your muffins a really rich chocolate flavor – without any espresso powder or melted chocolate!
Yup, it’s true… You can make delicious chocolate muffins without espresso (and cupcakes and brownies too!) – and I personally think that’s best! My taste buds are sensitive enough that adding espresso just makes chocolate-flavored baked treats taste like mochas instead… Still delicious – but just not the pure chocolate flavor I want! 😉
The type of cocoa powder you use is really important! To make the best healthy chocolate muffins, use regular unsweetened cocoa powder (also called “natural cocoa powder” or “natural unsweetened cocoa powder”). I do not recommend substituting Dutched or special dark cocoa powder. These latter two have a different acidity level, which affects the taste and texture of your muffins. They also don’t provide as rich or as strong of a chocolate flavor in this recipe.
Hint: I like using Hershey’s regular unsweetened cocoa powder (it’s made from 100% cacao!) to make these muffins because it’s affordable, easy to find in most US stores, and has a good chocolate flavor.
Flour. To make these chocolate muffins healthier, I used white whole wheat flour. I know… That sounds strange – and almost like an oxymoron! But I promise such a thing exists, and it’s not just a combination of white (aka all-purpose!) flour and regular whole wheat flour.
Here in the US, the majority of wheat that’s grown is a heartier variety of red wheat, and that’s what’s used to make regular whole wheat flour. In contrast, white whole wheat flour is made by finely grinding white wheat (hence the name!), and it has a lighter appearance, taste, and texture. Both regular and white whole wheat flour have the same health benefits (like extra fiber!), but white whole wheat flour’s softer taste and texture allows both the rich flavor and really moist texture of your healthy chocolate muffins to truly shine.
Hint: It’s similar to the difference between red and green grapes! They have the same health benefits, just a slightly different taste and texture.
Tip: If you’d like to make your healthy chocolate muffins gluten free, then see the Notes section of the recipe! I’ve included my top recommendations there.
Egg whites. The egg whites’ protein helps provide structure, both during and after baking. That protein helps the muffins maintain their shape while cooling. Without both egg whites, the muffins tend to collapse while cooling and turn out much denser… Not good!
So yes – for the best soft and tender texture, you do need to use both egg whites!
Greek yogurt. If you’ve browsed through my recipes before, you already know… Greek yogurt is one of my favorite ingredients in healthy baking – and my secret to moist muffins! To make these muffins, you’re only using a mere ½ tablespoon of butter or oil, so Greek yogurt adds the same moisture to the batter as extra butter or oil – but for a fraction of the calories. It also gives your healthy chocolate muffins a protein boost!
Sweetener. To help make these chocolate muffins more low calorie, I used liquid stevia to sweeten them. Stevia is a plant-based, no-calorie sweetener that’s “clean eating” friendly. It’s also highly concentrated. You only need 2 ½ teaspoons to sweeten this entire batch of muffins!
Tip: By using stevia, it means the batter of your healthy chocolate muffins is sugar free!
Many stevia brands and products have different sweetness levels, so they’re not necessarily a 1-for-1 substitute for one another. For the best results, I highly recommend using the same one I do. I love its sweet flavor and don’t notice any strange aftertaste like with some other stevia products. You can find it in many health oriented grocery stores, but I buy it online here because that’s the best price I’ve found. (You’ll also use it in all of these recipes of mine too. I promise it’s not a “one-time use” ingredient!)
Tip: I know stevia isn’t an ingredient that everyone can find or enjoys, so I’ve also included some alternative sweetener options in the Notes section of the recipe!
Mini chocolate chips. I love using mini chocolate chips because their smaller size ensures every bite contains at least one morsel – if not more! Some brands taste and melt better than others. Ghirardelli’s mini chocolate chips are one of my favorites for both taste and texture, and Target’s own Good & Gather mini chocolate chips melt incredibly well too. (When I used those, the ones hidden inside of these muffins stayed a little gooey and melty, even once the muffins had fully cooled!)
Hint: To make your chocolate muffins completely sugar free, use sugar free mini chocolate chips – like my homemade mini chocolate chips!
Tip: Save some of the mini chocolate chips to press into the tops of the batter just before baking! I think it gives them a pretty finishing touch… And it also makes them look even more tempting! 😉
HOW TO MAKE THE ULTIMATE HEALTHY CHOCOLATE MUFFINS
Now that you have all of your ingredients ready, let’s go over how to make the best healthy chocolate muffins! This recipe is mostly simple and straightforward, but I still have some tips for you.
Measure the ingredients correctly. I might sound like a broken record… But this is extremely important, especially for the cocoa powder and flour. Too much of either ingredient will make your muffins crumbly or dry, and too much cocoa powder can make them taste bitter. So for the best moist, rich, and chocolaty muffins, measure your ingredients the correct way!
If you have a kitchen scale, now is a great time to pull it out! I own this one, and I use my kitchen scale every time I bake because (a) it ensures my baked goods turn out with the perfect taste and texture every time and (b) it usually results in fewer dishes to wash. (Always a good thing, in my book! 😉 )
If you don’t have a kitchen scale, then use this method for measuring. It’s similar to the traditional “spoon-and-level” method, but one key difference in my measuring approach helps guard against accidentally adding too much flour or cocoa powder even more.
Skip the mixer. That’s right – put away your stand mixer or hand-held mixer! Both of these tend to over-mix “healthy” batters that are low fat or low sugar (or both!), like this chocolate muffin batter. Over-mixing usually results in a tough, rubbery, or gummy texture. Not exactly the texture you want in breakfast muffins!
Therefore, for the best soft and moist chocolate muffins, make this batter by hand. Use a whisk where explicitly instructed, and use a fork for everything else.
Why a fork? And not a wooden spoon or spatula?
The space between the tines of the fork allows for the ingredients to pass through and mix more efficiently. This helps prevent over-mixing too!
Use alternating additions. This is just a shorthand way of saying “switch between gently stirring in small amounts of the dry ingredients and the milk.” It’s a common technique used to make cake and cupcake batters, and I like to use it when making muffins too. Just like with making the batter by hand (with a fork!), alternating additions also help prevent over-mixing and result in a better moist and tender muffin texture.
Coat the liners with cooking spray. Low fat muffin batters with minimal amounts of butter or oil (like this one!) tend to stick to liners like superglue. However, if you generously coat those paper or foil liners with nonstick cooking spray before dolloping in the batter, they’ll peel away much more easily from the muffins!
Tip: If you forget to coat the liners – or don’t do a very thorough job – then seal the muffins inside of an airtight container or zip-topped bag and refrigerate them for 24+ hours. This helps loosen the liners a bit more!
Bake. Your healthy chocolate muffins are done when the tops feel firm to the touch and a toothpick inserted into the center comes out clean or with some crumbs attached. Don’t forget to press some mini chocolate chips into the tops of the batter just before popping the pan in the oven to make your homemade ones look just like bakery-style muffins too!
FAQS ABOUT THE ULTIMATE HEALTHY CHOCOLATE MUFFINS
Are these healthy chocolate muffins gluten free, sugar free, or clean eating?
Yes! When made as written, these chocolate muffins are sugar free and clean eating, as well as low fat and low calorie. I’ve also included my top recommendations for how to make them gluten free in the Notes section of the recipe!
How do you make chocolate muffins moist?
Five key ways! (1) Greek yogurt, (2) measure all ingredients correctly, (3) make the batter by hand, (4) use alternating additions, and (5) don’t overbake them. See the “Ingredients” and “How to Make” sections of my blog post above for more info about each one!
What’s the best cocoa powder for chocolate muffins?
Natural cocoa powder! It’s also called regular unsweetened cocoa powder. I don’t recommend using Dutched or special dark cocoa powder. See the “unsweetened cocoa powder” header above for more info about why!
Can I make my chocolate muffins sweeter?
Absolutely! I realize not everyone loves dark chocolate as much as my family and I do. 😉 See the Notes section of the recipe for my recommendations about how to make these healthy chocolate muffins sweeter!
Can I substitute a different sweetener?
Yes! I’ve included quite a few alternatives in the Notes section of the recipe. You’ll need to adjust the amount of sweetener, as well as the milk, depending on the sweetener that you choose.
How should I store these healthy chocolate muffins? And how long do they keep?
Pop any leftover muffins into an airtight container, and place that in the refrigerator. When stored like this, your muffins should last for at least five days – if not longer!
Can I freeze these healthy chocolate muffins?
Yes! They freeze really well. If you’ve used liners, peel those off first. (They tend to stick a lot more after the muffins have been reheated or thawed.) I like to reheat individual frozen muffins in the microwave on 30% power until warmed all the way through. When thawed like this, the chocolate chips turn melty and gooey, and the muffins almost taste freshly baked!
Ready to make your own? And when you do, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! 🙂 ) I’d love to see your healthy chocolate muffins!
The Ultimate Healthy Chocolate Muffins
- 1 ¼ cups (100g) unsweetened cocoa powder (measured like this)
- 1 ¼ cups (150g) white whole wheat flour or gluten-free* flour (measured like this)
- 1 ½ tsp baking powder
- ¾ tsp baking soda
- ¼ tsp salt
- ½ tbsp (7g) unsalted butter or coconut oil, melted and cooled slightly
- 2 large egg whites, room temperature
- 2 tsp vanilla extract
- 2 ½ tsp liquid stevia (see Notes!)
- ½ cup (120g) plain nonfat Greek yogurt
- 1 cup + 2 tbsp (270mL) nonfat milk, divided
- ¼ cup (56g) miniature chocolate chips, divided
- Preheat the oven to 350°F, and coat 12 muffin cups with nonstick cooking spray. (If using liners, then line 12 muffins cups with liners and generously coat them with cooking spray.)
- In a medium bowl, whisk together the cocoa powder, flour, baking powder, baking soda, and salt. In a separate bowl, whisk together the coconut oil or butter, egg whites, vanilla extract, and liquid stevia. Add in the Greek yogurt, stirring until no large lumps remain. Stir in ½ cup + 2 tablespoons of milk. Alternate between adding the flour mixture and remaining milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.) Set aside ½ tablespoon of miniature chocolate chips, and gently fold in the rest.
- Divide the batter between the prepared muffin cups, and gently press the reserved miniature chocolate chips on top. Bake at 350°F for 21-24 minutes or until the tops feel firm to the touch and a toothpick inserted into the center comes out clean (or with a few crumbs attached). Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.
View Nutrition Information + Weight Watchers Points
You may also like Amy’s other recipes…
♡ The Ultimate Healthy Blueberry Muffins
♡ The Ultimate Healthy Apple Muffins
♡ The Ultimate Healthy Banana Muffins
♡ The Ultimate Healthy Lemon Poppy Seed Muffins
♡ The Ultimate Healthy Pumpkin Muffins
♡ Healthy Triple Chocolate Scones
♡ Healthy Flourless Chocolate Oatmeal Breakfast Cookies
♡ Healthy Chocolate Pancakes
♡ …and the rest of Amy’s healthy breakfast recipes!
I also used the same cocoa powder you recommended, the Hershey unsweetened cocoa powder.
Thanks for sharing this additional information, Stacey! I looked up Kroger brand stevia, and it looks as if they offer 4 stevia products: (a) a granulated stevia sweetener blend in a jar, (b) a powdered stevia sweetener blend in a bag, (c) stevia packets, and (d) a squeeze bottle. Which one of these did you use? (Each of these products has a different sweetness level and concentration, so I want to make sure I know the exact Kroger product that you used to make these muffins! 🙂 )
Also, just to confirm, did you use 2 ½ teaspoons of the Kroger stevia product?
Janice Bramston says...
What is the nutritional values? Thank you 😊
Stacey @ Amy's Healthy Baking says...
We really appreciate your interest in our recipe, Janice! The full nutrition information is included directly underneath the recipe box. I know it can be really easy to miss though! 😉 We’d love to hear what you think of these muffins if you try making this recipe!