Healthy & Delicious Chocolate Applesauce Muffins: Your New Favorite Breakfast Treat
Indulge in these incredibly moist and richly flavored chocolate muffins, secretly made healthier with wholesome applesauce and creamy Greek yogurt. For an extra touch of deliciousness, we’ve even folded in some delightful peanut butter chips – though they’re optional, they truly elevate the experience!

Today marks a truly special occasion for my husband and me: a well-deserved day off! We’ve carved out this precious time just for ourselves, free from major housework (though we might tackle a small task or two) and, most importantly, with our little one embarking on a fun-filled adventure with Grandma and Grandpa. It feels like ages since we’ve had a day entirely to ourselves, especially after what feels like endless weeks of working tirelessly. I’m incredibly excited about the prospect of reconnecting, relaxing, and even enjoying a lovely dinner out tonight.
Before diving into our much-anticipated day of relaxation, I simply had to share this fantastic recipe for Chocolate Applesauce Muffins. These aren’t just any muffins; they’re a delightful revelation that makes having chocolate for breakfast an entirely guilt-free pleasure. Combining the natural sweetness and moisture of unsweetened applesauce with the rich, tender texture of plain Greek yogurt, these muffins strike the perfect balance between indulgence and healthy eating. Each muffin comes in at around 130 calories, making them a smart choice for starting your day or for a satisfying, wholesome snack.
Why These Chocolate Applesauce Muffins Will Become Your Favorite
These muffins aren’t just a treat; they’re a culinary masterpiece perfect for busy mornings, afternoon pick-me-ups, or even a light dessert. Here’s why they’re destined to become a staple in your recipe collection:
- Naturally Sweetened & Healthier: Unsweetened applesauce is a brilliant natural sweetener and a wonderful substitute for some of the butter or oil typically found in muffin recipes. It provides a delicate sweetness and incredible moisture, significantly reducing the need for excessive added sugars and fats. This means you get to enjoy a truly delicious chocolate muffin with fewer calories and a more wholesome nutritional profile.
- Unbeatable Moist & Tender Texture: Thanks to the winning combination of applesauce and creamy Greek yogurt, these muffins boast an exceptionally moist, fluffy, and tender crumb. You can say goodbye to dry, crumbly muffins; every single bite of these is pure, melt-in-your-mouth bliss. The yogurt also adds a subtle tang that perfectly balances the sweetness.
- Rich, Deep Chocolate Flavor: Don’t let the “healthy” aspect fool you into thinking these lack flavor. With a generous amount of unsweetened cocoa powder and plenty of chocolate chips, these muffins deliver a deep, satisfying chocolatey punch that will undoubtedly satisfy even the most intense cacao cravings. It’s a true chocolate lover’s dream!
- Kid-Approved and Family-Friendly: My 7-year-old absolutely adored these muffins! They vanished from our freezer remarkably quickly, a true testament to their deliciousness and broad appeal. It’s a wonderful and easy way to sneak some fruit into your children’s diet while offering a treat they’ll genuinely love.
- Incredibly Freezer-Friendly: Just like I often do, you can easily bake a larger batch and freeze the extras for later. These muffins reheat beautifully, maintaining their moist texture and rich flavor, making them absolutely perfect for convenient meal prep, quick breakfasts on the go, or impromptu sweet cravings.
- Highly Versatile for Customization: While I couldn’t resist adding a handful of peanut butter chips for an extra layer of salty-sweet deliciousness, these muffins are highly adaptable. Feel free to easily customize them with your favorite mix-ins, from different types of chocolate chips to various nuts or dried fruits.

The Nutritional Power of Applesauce and Greek Yogurt in Baking
What truly sets these chocolate muffins apart, beyond their irresistible flavor, is the intelligent use of applesauce and plain Greek yogurt. These two ingredients aren’t just additions; they play pivotal roles in enhancing the muffin’s texture, flavor, and overall nutritional profile.
- Applesauce: When used unsweetened, applesauce serves as a fantastic natural sweetener and a remarkable fat replacer. It injects a considerable amount of moisture into the batter, which is essential for achieving that wonderfully tender and soft crumb we all desire in a high-quality muffin. Furthermore, it contributes a subtle, natural fruity note that beautifully complements the deep chocolate flavor, all while significantly reducing the need for excessive amounts of added sugars and unhealthy fats.
- Plain Greek Yogurt: This ingredient is an absolute powerhouse in baking. It dramatically boosts the protein content of the muffins, making them more satisfying and helping to keep you feeling fuller for longer, which is ideal for a breakfast item. The yogurt’s natural acidity reacts with the baking soda in the recipe, creating a lighter, fluffier texture and contributing to a higher rise. Plus, it further enhances the overall moistness and richness, imparting a luxurious, almost decadent mouthfeel to the muffins without adding extra fat.
Together, these carefully selected ingredients transform a seemingly simple chocolate muffin into a wholesome, yet utterly delectable and nourishing baked good that you can truly feel good about enjoying, whether it’s for breakfast, a snack, or a healthier dessert option.

Essential Tips for Baking the Perfect Chocolate Applesauce Muffins
Achieving bakery-quality muffins right in your own kitchen is easier than you might think, especially when you keep a few key baking tips in mind:
- Avoid Overmixing the Batter: This is arguably the most crucial rule for ensuring your muffins turn out tender and moist. Once you combine the wet and dry ingredients, mix only until they are *just* incorporated. A few small lumps in the batter are perfectly normal and even desirable; overmixing develops the gluten in the flour, which leads to tough, chewy muffins.
- Ensure Room Temperature Ingredients: While some recipes can be forgiving, using room temperature eggs and Greek yogurt helps them emulsify and incorporate more smoothly and evenly into the batter. This creates a more uniform texture in your finished muffins.
- Prepare Your Muffin Tins Thoroughly: Even if you’re using paper liners, it’s a good idea to lightly spray the muffin tin cups with cooking oil. This acts as a double safeguard, preventing any sticking and ensuring your beautifully baked muffins release cleanly and effortlessly from the pan.
- Fill Muffin Cups Correctly: For those beautifully domed, professional-looking muffin tops, aim to fill your muffin cups about two-thirds to three-quarters full. Resist the temptation to overfill, as this can cause the batter to overflow during baking, creating a messy situation and unevenly shaped muffins.
- Get Creative with Your Mix-ins: While the addition of peanut butter chips offers a fantastic flavor profile, feel completely free to experiment and customize! White chocolate chips, dark chocolate chunks, chopped nuts (like walnuts or pecans), dried cranberries, or even a hint of ground cinnamon or nutmeg can all add delightful variations and personalize your muffins.
- Proper Cooling is Paramount: Once your muffins are out of the oven, allow them to cool in the pan for about 5 minutes. This brief resting period helps them set up properly. After 5 minutes, carefully remove them from the pan and transfer them to a wire rack to cool completely. This prevents any trapped steam from making the bottoms soggy.
Storage and Freezing Instructions for Maximum Freshness
These Chocolate Applesauce Muffins are not only delicious but also incredibly convenient for meal prepping or simply ensuring you always have a delightful, homemade treat on hand:
- At Room Temperature: Store your completely cooled muffins in an airtight container at room temperature. They will remain wonderfully fresh and moist for up to 2-3 days.
- In the Refrigerator: For extended freshness, especially if your kitchen tends to be on the warmer side, you can store them in an airtight container in the refrigerator for up to 5 days. Just bring them to room temperature or warm them slightly before serving.
- For Freezing: These muffins are exceptionally freezer-friendly! Once they have cooled down completely to room temperature, arrange them in a single layer on a baking sheet and freeze until they are solid (this usually takes about 1-2 hours). Once frozen, transfer the muffins to a freezer-safe bag or an airtight container, making sure to remove as much air as possible to prevent freezer burn. They will maintain their quality and flavor beautifully for up to 3 months. To enjoy, simply thaw them at room temperature for a few hours, or gently warm them in the microwave for a quick and deliciously fresh-tasting snack.
Looking for even more muffin inspiration to fill your breakfast table or snack drawer? Be sure to check out the incredible variety of 50 Muffins that have been shared on our site before, all conveniently gathered in one place. Whether you’re craving something sweet, savory, or somewhere delightfully in between, you’re bound to find a muffin recipe that you and your family will absolutely love:
- Peanut Butter and Jelly Muffins: A nostalgic and comforting twist on a beloved classic flavor combination, perfect for kids and adults alike.
- Cinnamon Roll Muffins: Enjoy all the warm, spiced deliciousness of a classic cinnamon roll, conveniently baked into a portable muffin form.
- Triple Chocolate Muffins: For the ultimate chocolate lover, this extra indulgent treat features three kinds of chocolate for an unforgettable experience.

Chocolate Applesauce Muffins
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Equipment
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Kitchen Aid Stand Mixer
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Muffin Tins
Ingredients
- 1 1/2 cups unsweetened applesauce
- 2/3 cup granulated sugar
- 1/4 cup butter, melted and cooled slightly
- 1/4 cup plain Greek yogurt
- 2 large eggs
- 1 3/4 cups all-purpose flour
- 1/2 cup unsweetened cocoa powder
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 3/4 cup chocolate chips
- 1/4 cup mini chocolate chips, for topping
Instructions
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Preheat oven to 350F (175°C). Prepare muffin tins with cooking spray or paper liners. This recipe yields approximately 15 muffins.
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In a large bowl, mix together the unsweetened applesauce, granulated sugar, melted butter, plain Greek yogurt, and large eggs until the mixture is smooth and all ingredients are well combined.1/4 cup butter, 1/4 cup plain Greek yogurt, 2/3 cup granulated sugar, 2 large eggs, 1 1/2 cups unsweetened applesauce
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In a separate, medium-sized bowl, whisk together the all-purpose flour, unsweetened cocoa powder, baking powder, baking soda, and salt until thoroughly combined.1 3/4 cups all-purpose flour, 1/2 cup unsweetened cocoa powder, 1 teaspoon baking powder, 1 teaspoon baking soda, 1/2 teaspoon salt
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Gradually add the dry flour mixture to the wet apple sauce mixture. Mix gently until it is just barely combined. Be careful not to overmix, as this can lead to tough muffins.
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Gently fold in the chocolate chips (and peanut butter chips, if using) until evenly distributed throughout the batter.3/4 cup chocolate chips
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Fill each muffin cup about three-quarters full with the batter. Sprinkle the remaining mini chocolate chips evenly over the top of each muffin for a beautiful finish. Bake for 18-20 minutes, or until a wooden skewer or toothpick inserted into the center of a muffin comes out clean.1/4 cup mini chocolate chips
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Allow the muffins to cool in the pan for 5 minutes before carefully removing them to a wire rack to cool completely. Enjoy warm or at room temperature!
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Additional Info
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