Healthy Pumpkin Chocolate Chip Muffins: Your Best Fall Snack & Breakfast
These easy, healthy pumpkin chocolate chip muffins are the ultimate snack for fall, merging wholesome ingredients with irresistible flavor!

Embrace Autumn with Deliciously Healthy Pumpkin Chocolate Chip Muffins
Ring in the fall season with these incredibly **healthy pumpkin chocolate chip muffins**! I don’t know about you, but autumn is my absolute favorite time of year. There’s something magical about the crisp air, vibrant foliage, and of course, the comforting flavors that come with it. Give me all the pumpkin bread, apple crisp, cozy clothes, and cool mornings. If only it could be fall year-round, now that would truly be amazing!
These easy and healthy pumpkin muffins are meticulously **made with lighter ingredients**, ensuring you can indulge without guilt. We use nourishing components like Greek yogurt, wholesome whole wheat flour, and natural pumpkin puree. What’s more, they are completely oil-free and come in at less than 150 calories each, making them a perfect guilt-free treat for any time of day. The combination of warm pumpkin spice and sweet chocolate chips creates a flavor profile that perfectly captures the essence of autumn.

Essential Ingredients for Your Healthy Pumpkin Chocolate Chip Muffins
Crafting these delectable muffins requires a careful selection of ingredients that contribute to both their incredible taste and their healthier profile. Here’s a detailed look at what you’ll need:
- Plain Greek Yogurt: This is the secret weapon for moisture and protein. Opt for the unsweetened, 0% fat variety to keep things light, or full-fat for a richer texture. It replaces oil, keeping the muffins deliciously moist without the added fat.
- Pumpkin Puree: Ensure you grab pure canned pumpkin, not pumpkin pie filling. Pumpkin puree provides natural sweetness, a beautiful orange hue, and a wealth of vitamins and fiber, making these muffins genuinely healthy.
- Eggs: Act as a binder, adding structure and richness to the muffins.
- Whole Wheat Flour: This provides a heartier texture and a significant boost of fiber compared to all-purpose flour, making your muffins more filling and nutritious.
- Rolled Oats: Also known as old-fashioned oats, these add a delightful chewiness and additional fiber, contributing to the muffins’ healthy profile.
- Brown Sugar: A touch of brown sugar offers a deep, molasses-like sweetness that complements the pumpkin spice perfectly. While these are healthier muffins, a little natural sweetness enhances the flavor without overdoing it.
- Pumpkin Pie Spice: The quintessential fall spice blend! This gives your muffins that signature warm, aromatic flavor.
- Vanilla Extract: A splash of vanilla enhances all the other flavors, adding a comforting depth.
- Salt: A pinch of salt balances the sweetness and brings out the vibrant flavors of the pumpkin and spices.
- Baking Soda & Baking Powder: These leavening agents work together to ensure your muffins rise beautifully, resulting in a light and fluffy texture.
- Mini Chocolate Chips: The classic pairing with pumpkin! Mini chips distribute more evenly throughout the batter, ensuring every bite has a delightful chocolatey surprise.

Step-by-Step Guide: How to Bake Healthy Pumpkin Chocolate Chip Muffins
Creating these delightful muffins is simpler than you might think. Follow these straightforward steps for perfect results every time:
Step 1: Combine Wet Ingredients. In a large mixing bowl, thoroughly **whisk together the wet ingredients**: plain Greek yogurt, pumpkin puree, eggs, brown sugar, and vanilla extract. Whisk until the mixture is smooth and well combined. This forms the moist base of your muffins.
Step 2: Mix Dry Ingredients. In a separate, medium-sized bowl, **whisk the dry ingredients**: whole wheat flour, rolled oats, pumpkin pie spice, salt, baking soda, and baking powder. This ensures all the leavening agents and spices are evenly distributed, preventing pockets of unmixed ingredients.


Step 3: Combine Wet and Dry, then Add Chocolate. Gently **add the wet ingredients to the dry ingredients**. Using a rubber spatula, mix until *just combined*. The key here is to avoid overmixing the batter, as this can lead to tough muffins. A few lumps are perfectly fine! Once combined, **fold in the mini chocolate chips** with a few gentle stirs, ensuring they are distributed throughout the batter.


Step 4: Fill Muffin Cups and Garnish. **Line 12 standard muffin cups** with parchment paper muffin liners (these are a game-changer for oil-free baking!). Evenly **distribute the muffin batter** into the prepared muffin cups. For an extra touch, sprinkle on a few additional mini chocolate chips over the tops of the muffins before baking. This makes them look even more inviting.
Step 5: Bake to Perfection. Preheat your oven to 400°F (200°C). Bake the healthy pumpkin muffins **at 400 degrees Fahrenheit for 15-17 minutes**, or until a toothpick inserted into the center of a muffin comes out clean. The high initial temperature helps create that signature muffin top, then the muffins cook through perfectly. Let them cool in the pan for a few minutes before transferring to a wire rack to cool completely.


The Secret to Non-Stick Muffins: Parchment Paper Liners
Because these healthy pumpkin muffins are intentionally made without oil, you might encounter an issue with them sticking to traditional muffin liners. The incredibly easy and effective solution for this is to invest in **parchment paper muffin liners**. You can find these at most grocery stores or online. Parchment liners have truly changed my baking life! Absolutely nothing will stick to them, ensuring your beautifully baked muffins slide out effortlessly every time, leaving no delicious crumbs behind. If you only have regular paper liners, a quick spray with cooking oil will help, but parchment is truly superior for oil-free recipes.

These healthy pumpkin chocolate chip muffins are versatile enough to be enjoyed for a wholesome breakfast, yet decadent enough to satisfy your sweet tooth as a delicious treat. The key to their incredibly fluffy and moist texture, despite being oil-free, lies in the generous use of **Greek yogurt**. It provides a rich creaminess and adds a wonderful protein boost, making these muffins both satisfying and good for you.

Why You’ll Love These Healthy Pumpkin Chocolate Chip Muffins
Beyond being incredibly delicious, these pumpkin chocolate chip muffins offer a range of benefits that make them a staple in any healthy kitchen, especially during fall:
- Guilt-Free Indulgence: With whole wheat flour, Greek yogurt, and no added oil, these muffins are significantly lighter than traditional versions, allowing you to enjoy a sweet treat without the guilt.
- Packed with Nutrients: Pumpkin is rich in Vitamin A, fiber, and antioxidants, while whole wheat flour adds more fiber and nutrients. Greek yogurt contributes protein, making these muffins a nutritious choice.
- Perfect for Any Time of Day: Low in sugar and high in protein, they’re ideal for a satisfying breakfast, a quick grab-and-go snack, or a healthier dessert option to curb your sweet tooth.
- Easy to Make: The recipe is straightforward, requiring minimal effort and common pantry ingredients. Even beginner bakers can achieve fantastic results.
- Flavorful & Moist: Despite being healthy, they don’t compromise on flavor or texture. They are wonderfully moist, spiced just right, and dotted with melty chocolate chips.
Tips for Perfect Pumpkin Chocolate Chip Muffins Every Time
Achieving bakery-quality muffins at home is easy with a few simple tips:
- Don’t Overmix: This is crucial for tender muffins. Mix the wet and dry ingredients only until just combined. A few lumps are fine! Overmixing develops gluten, leading to tough muffins.
- Room Temperature Ingredients: Ensure your eggs and Greek yogurt are at room temperature. This helps them incorporate more smoothly into the batter, leading to a more uniform texture.
- High Initial Heat: Starting the oven at 400°F (200°C) for the first few minutes (as in the recipe) helps the muffins rise quickly and develop those beautiful, domed tops before reducing the temperature for even cooking.
- Use Parchment Liners: As mentioned, these are essential for oil-free muffins to prevent sticking. If you don’t have them, generously grease regular paper liners or the muffin tin itself.
- Fill Muffin Cups Generously: This recipe makes generous muffins. Filling the cups almost to the top will yield large, satisfying muffins with lovely domes.
- Check for Doneness: The toothpick test is your best friend. Insert a toothpick into the center of a muffin; if it comes out clean, they’re ready. Avoid overbaking, which can dry them out.
Variations & Serving Suggestions
These healthy pumpkin chocolate chip muffins are fantastic as is, but feel free to get creative with variations and serving ideas:
Customizing Your Muffins:
- Add Nuts: For extra crunch and healthy fats, fold in chopped pecans or walnuts along with the chocolate chips.
- Extra Spice: If you love a bolder spice flavor, add a pinch of ground cinnamon, nutmeg, or ginger to the dry ingredients.
- Different Chocolates: Experiment with dark chocolate chunks, white chocolate chips, or a mix of different chocolates for varying flavor profiles.
- Dried Fruit: A handful of dried cranberries or raisins can add a chewy texture and a touch of tartness.
- Gluten-Free Option: You can often substitute whole wheat flour with a 1:1 gluten-free baking blend that contains xanthan gum.
Serving Ideas:
- Warm with Coffee or Tea: A classic pairing for a cozy breakfast or an afternoon pick-me-up.
- With a Dollop of Yogurt: For an extra protein boost, serve a warm muffin with a spoonful of plain Greek yogurt.
- Nut Butter Spread: A smear of almond or peanut butter can add richness and a healthy fat component.
- As a Healthy Dessert: These muffins are sweet enough on their own but can be elevated with a light dusting of powdered sugar or a drizzle of maple syrup.

Discover More Irresistible Pumpkin Recipes for Fall
If you’re as big a fan of pumpkin as we are, you’ll love exploring these other delicious fall-inspired recipes. From cookies to pies, there’s a pumpkin treat for every craving!
- Gluten Free Pumpkin Pie Cookies
- Pumpkin Banana Bread
- Healthy Pumpkin Truffles
- Pumpkin Cream Pie
- No Bake Pumpkin Cheesecake Bars
- Gluten Free Pumpkin Pie

Frequently Asked Questions About Healthy Pumpkin Chocolate Chip Muffins
Leftover muffins can be stored in an airtight container at room temperature for up to 2 days, or in the refrigerator for 3-5 days to maintain freshness, especially due to the Greek yogurt. They also freeze wonderfully!
You can certainly use other types of Greek yogurt. Whole plain Greek yogurt will add a bit more fat and richness, making the muffins even more tender. Keep in mind that vanilla Greek yogurt has added sweetener, which will make your muffins sweeter, so you might want to slightly reduce the brown sugar if you use it.
No, these are distinctly different. Canned pumpkin puree should contain just one ingredient: pumpkin. Pumpkin pie filling, on the other hand, comes pre-seasoned with added spices and sweeteners, making it unsuitable as a direct substitute for pure pumpkin in recipes like this.
Absolutely! These muffins are perfect for meal prepping. You can bake a batch on Sunday and enjoy them throughout the week for quick breakfasts or snacks. Store them as directed above.
Yes, these muffins freeze beautifully! Once completely cooled, wrap individual muffins tightly in plastic wrap, then place them in a freezer-safe bag or container. They can be frozen for up to 3 months. Thaw at room temperature or warm gently in the microwave.


Healthy Pumpkin Chocolate Chip Muffins
Joy Shull
10 minutes
15 minutes
25 minutes
12
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Ingredients
-
1 cup plain 0% greek yogurt -
1 cup canned pumpkin puree -
2 eggs -
1 1/4 cups whole wheat flour -
1/2 cup rolled oats -
1/3 cup brown sugar -
1 teaspoon pumpkin pie spice -
1 tablespoon vanilla extract -
1/4 teaspoon salt -
1/4 teaspoon baking soda -
1 teaspoon baking powder -
1/2 cup mini chocolate chips
Instructions
-
In a medium sized bowl, whisk together the wet ingredients: greek yogurt, pumpkin, eggs, brown sugar, and vanilla extract until smooth.
-
In a separate bowl, whisk the dry ingredients: whole wheat flour, rolled oats, pumpkin pie spice, salt, baking soda, and baking powder until well combined.
-
Add the wet ingredients to the dry ingredients, mixing with a rubber spatula until just combined (do not over mix to keep muffins tender).
-
Gently fold in the mini chocolate chips until evenly distributed.
-
Line 12 muffin cups with parchment paper muffin liners (these will not stick like regular muffin liners). If you use regular muffin liners, spray them generously with cooking spray to avoid sticking.
-
Distribute the muffin batter evenly into the prepared muffin cups (these will be large muffins).
-
Sprinkle on additional mini chocolate chips over the tops of each muffin for an appealing finish.
-
Bake the pumpkin muffins in a preheated oven at 400 degrees F for 15-17 minutes, or until a toothpick inserted into the center comes out clean. Let cool slightly before serving.
Video
Nutrition
Calories:
148
kcal
,
Carbohydrates:
25
g
,
Protein:
5
g
,
Fat:
3
g
,
Saturated Fat:
1
g
,
Polyunsaturated Fat:
0.4
g
,
Monounsaturated Fat:
0.4
g
,
Trans Fat:
0.02
g
,
Cholesterol:
29
mg
,
Sodium:
131
mg
,
Potassium:
144
mg
,
Fiber:
2
g
,
Sugar:
12
g
,
Vitamin A:
3236
IU
,
Vitamin C:
1
mg
,
Calcium:
69
mg
,
Iron:
1
mg
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