Discover the delightful taste of autumn with these incredibly healthy and flavor-packed Butternut Squash Muffins. Infused with the sweet crunch of apples, the comforting warmth of cinnamon, and the nutty goodness of walnuts, these muffins are a guilt-free pleasure. What sets them apart? We swap traditional oil for protein-rich Greek yogurt, making them a fantastic choice for a nutritious breakfast, a satisfying mid-day snack, or even a light dessert.

Delicious & Healthy Butternut Squash Muffins with Apples & Walnuts
Fall is synonymous with cozy flavors, and while pumpkin often steals the show, we’re here to champion the often-underestimated butternut squash. These muffins offer a unique twist, combining the earthy sweetness of butternut squash with the crisp tartness of apples, all balanced by a blend of warm spices. Far from being just a seasonal treat, their nutritional profile makes them a smart choice year-round.
You might be wondering, “Why butternut squash when there are so many fantastic pumpkin muffin recipes out there?” Thatâs an excellent question, and we’re thrilled to share our compelling reasons:
- Effortless Puree Preparation: Youâve discovered the sheer simplicity of making crock-pot butternut squash puree and now you have an abundance to enjoy! This recipe is a perfect way to utilize that delicious, homemade goodness.
- A Unique Fall Flavor Profile: If you’re not a pumpkin fanatic but still crave a wholesome, fall-inspired baked good, butternut squash offers a subtly sweet and incredibly moist alternative. Its mild flavor pairs beautifully with a variety of spices and additions.
- A Welcome Change of Pace: Perhaps you’ve indulged in a few too many healthy chocolate pumpkin muffins recently and are looking for something new and equally delicious. These butternut squash muffins provide that much-needed variety without sacrificing health benefits.
- Protein-Packed & Veggie-Loaded: Needing a substantial, energizing snack to combat that dreaded mid-day slump? These muffins are loaded with nutrient-dense butternut squash and boast a significant protein boost from Greek yogurt, helping you stay full and focused.
- Irresistibly Appealing: Let’s be honest â they look absolutely delicious. And trust us, they taste even better!
These are all compelling reasons why our family canât get enough of these delightful muffins. And rest assured, while we love a good pumpkin recipe, you won’t find any pumpkin purists complaining about these!
This recipe is a delightful variation of our popular Healthy Pumpkin Muffins with Chocolate Chips and proudly joins our collection of healthy, Greek yogurt-based muffin recipes, all designed to offer maximum flavor with minimal guilt.

Crafting the Perfect Butternut Squash Puree for Your Muffins
The foundation of these delicious muffins is fresh, flavorful butternut squash puree. You’ll need approximately 1 ½ cups for this recipe, and getting it ready is simpler than you might think. Here are a couple of excellent methods to prepare your puree:
- Cooking Your Butternut Squash:
- Slow Cooker Method (Our Favorite!): This is by far the easiest and most hands-off approach. Simply place a whole butternut squash (unpeeled and uncut) into your slow cooker. Cook on high for 3-4 hours or on low for 4-6 hours, until it’s incredibly tender. The skin will be soft, making it easy to remove and scoop out the flesh.
- Roasting Method: For a slightly deeper, caramelized flavor, roasting is an excellent choice. Cut the butternut squash in half lengthwise and scoop out the seeds. Place the halves face down on a baking sheet. Roast in a 375°F (190°C) oven for about 40-50 minutes, or until the flesh is fork-tender.
- Bake or Microwave Cubed Squash: If you’re short on time, many grocery stores offer fresh or frozen butternut squash cubes. You can easily bake them according to package directions or microwave them until soft. Just be sure to check the label for frozen squash to ensure it’s pure butternut squash with no added ingredients or seasonings.
- Mashing to Perfection: Once your butternut squash is cooked and cooled slightly, use a fork or a potato masher to mash the cooked flesh into a uniform consistency. It doesn’t need to be perfectly smooth â a few small lumps can add character to your muffins! However, if you desire an ultra-smooth puree, a quick whirl in a food processor will do the trick.
- Removing Excess Liquid: Butternut squash can sometimes hold a lot of moisture, which can affect the texture of your muffins. If your puree seems watery, place it in a fine-mesh strainer lined with cheesecloth for about 15-20 minutes to allow any excess liquid to drain before measuring out the required amount for your recipe. This step ensures your muffins aren’t too dense or gummy.
Important Note: When using frozen butternut squash, always double-check the label to confirm it is 100% pure butternut squash, not mixed with other vegetables or pre-seasoned. Unwanted ingredients can alter the flavor profile of your muffins.
By the way, if you find yourself with extra butternut squash puree, don’t let it go to waste! It’s incredibly versatile. Consider making a comforting dish like this Spicy Butternut Squash Soup, or simply season it with a touch of butter, salt, and pepper for a delicious side dish.

Elevating Flavor with Fresh Apples and Warm Spices
The addition of fresh apples is a game-changer in these butternut squash muffins. They not only impart a delightful extra layer of sweetness but also contribute to the muffins’ moist and tender crumb. Here are some expert tips for incorporating apples:
- Choosing the Right Apples: For optimal sweetness and flavor, we recommend opting for naturally sweet and crisp apple varieties. Excellent choices include Honeycrisp, Royal Gala, Fuji, or Ambrosia. These apples hold their shape well during baking and offer a pleasant texture.
- To Peel or Not to Peel?: This is often a matter of personal preference, but for these muffins, peeling the apples is entirely optional. We often leave the skin on, as it adds a lovely touch of color, extra fiber, and a rustic texture without being tough. Simply dice the apples into small, uniform pieces (about Ÿ to ½ inch cubes) with the skin on before adding them to the batter.
- Adjusting Sweetness: The natural sweetness of your chosen apple variety can influence the overall sugar content of your muffins. If you’re using a particularly sweet apple, you might be able to slightly reduce the amount of added sugar in the recipe, catering to your personal preference for sweetness.
- Spice it Up: While cinnamon is a must, don’t hesitate to enhance the spice profile. A pinch of nutmeg, a whisper of ground ginger, or a touch of allspice can truly elevate the autumn flavors and complement the butternut squash and apple beautifully.
- Walnuts for Texture and Nutrition: The chopped walnuts not only provide a delightful crunch but also contribute healthy fats and an extra layer of nutty flavor, making these muffins even more satisfying.
Be sure to follow the recipe closely to see how each ingredient comes together to create these perfect butternut squash muffins!

Health Benefits of Our Butternut Squash Muffins
These aren’t just delicious muffins; they’re a powerhouse of nutrition designed to support a healthy lifestyle. Let’s break down why these Butternut Squash Muffins with Apples and Walnuts are so good for you:
- Protein Power from Greek Yogurt: By substituting oil with Greek yogurt, we significantly boost the protein content while simultaneously reducing unhealthy fats. Greek yogurt also adds incredible moisture and tenderness to the muffins, resulting in a lighter texture without compromising flavor. Protein helps keep you feeling full and satisfied, making these an ideal snack or breakfast option.
- Nutrient-Rich Butternut Squash: Butternut squash is a fantastic source of vitamins and minerals. It’s especially high in Vitamin A (in the form of beta-carotene), which is crucial for vision, immune function, and skin health. It also provides a good dose of Vitamin C, potassium, and dietary fiber, promoting digestive health and contributing to a healthy heart.
- Fiber from Apples and Whole Grains: The inclusion of fresh apples, especially with their skins, adds valuable dietary fiber. Combined with whole wheat flour (or whole wheat pastry flour for a lighter texture), these muffins are rich in fiber, which aids digestion, helps regulate blood sugar levels, and contributes to satiety.
- Healthy Fats from Walnuts: Walnuts are an excellent source of omega-3 fatty acids, which are known for their anti-inflammatory properties and benefits for brain and heart health. They also provide healthy monounsaturated and polyunsaturated fats, adding to the overall nutritional value and rich texture of the muffins.
- Reduced Saturated Fat: With no added oil or butter, the saturated fat content in these muffins is kept to a minimum, making them a heart-healthy choice compared to many traditional muffin recipes.
Enjoying these butternut squash muffins means you’re not just savoring a delicious treat, but also nourishing your body with wholesome, beneficial ingredients.
Serving Suggestions & Storage Tips
These versatile Butternut Squash Muffins are perfect for a variety of occasions. Enjoy them:
- For Breakfast: Pair with a cup of coffee or tea for a quick, energizing start to your day. The protein from the Greek yogurt will help keep you satisfied until lunch.
- As a Healthy Snack: Grab one whenever hunger strikes between meals. Its combination of fiber, protein, and complex carbohydrates makes it a much better choice than processed snacks.
- With a Meal: Serve them as a wholesome side with a light brunch or a simple soup.
- As a Light Dessert: A slightly warmed muffin can be a comforting and healthier alternative to traditional desserts.
Storage Instructions:
- At Room Temperature: Store cooled muffins in an airtight container at room temperature for up to 2-3 days. Lining the container with a paper towel can help absorb excess moisture and prevent sogginess.
- In the Refrigerator: For longer freshness, refrigerate muffins in an airtight container for up to 5-7 days.
- Freezing for Later: These muffins freeze beautifully! Once completely cooled, place them in a single layer on a baking sheet and freeze for about an hour until solid. Then transfer them to a freezer-safe bag or container, removing as much air as possible to prevent freezer burn. They can be frozen for up to 3 months.
- Reheating: Thaw frozen muffins at room temperature or warm them in the microwave for 20-30 seconds, or in a preheated oven (300°F/150°C) for about 5-10 minutes, until heated through.
Explore More Healthy Muffin Recipes
If you love these butternut squash muffins, youâll be thrilled to discover other fantastic, healthy muffin recipes from our collection. Each one is crafted with wholesome ingredients and designed to fuel your day deliciously:
- Healthy Oatmeal Pumpkin Muffins or “Cups” {Gluten-free}
- Spaghetti Squash Au Gratin Casserole or Cups
- Healthy Greek Yogurt Banana Muffins
Would you like more easy, healthy, carb-conscious recipes?
đ Recipe: Butternut Squash Muffins with Apples

Butternut Squash Muffins with Apples
These delightful Butternut Squash Muffins, featuring apples, cinnamon, and walnuts, are packed with protein thanks to Greek yogurt replacing oil. They make a perfect healthy snack or wholesome breakfast.
Rating: 5 Stars from 2 votes
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Prep Time: 10 minutes | Cook Time: 25 minutes | Total Time: 35 minutes
Servings: 12 muffins
Author: Marjory Pilley
Ingredients
- 1 ½ cup white whole wheat flour or whole wheat pastry flour
- ½ cup sugar
- ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ½ teaspoon ground cinnamon
- 1 ½ cups butternut squash puree
- 1 egg, beaten
- 5.3 ounce non-fat Greek yogurt
- ½ cup apple, diced
- ½ cup walnuts, chopped
Instructions
- Preheat oven to 350 °F (175 °C).
- In a large bowl, combine the flour, sugar, baking powder, baking soda, salt, and cinnamon. Whisk well to ensure all dry ingredients are evenly distributed.
- Add the butternut squash puree, beaten egg, and Greek yogurt to the dry mixture. Stir gently with a spoon or spatula until just combined. Be careful not to overmix the batter.
- Carefully fold in the diced apple and chopped walnuts until they are evenly distributed throughout the batter.
- Fill muffin tins, coated with cooking spray or lined with paper liners, about two-thirds full. If using liners, a light spritz of cooking spray inside the liners can prevent sticking.
- Bake for 20-25 minutes, or until the muffins are firm to the touch and lightly golden brown on top. A wooden skewer or toothpick inserted into the center should come out clean.
- Allow the muffins to cool in the muffin tin for about 5 minutes before carefully transferring them to a wire rack to cool completely.
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