When the leaves start crunching underfoot and pumpkin-spice-everything suddenly appears on every menu, you know it’s time to bring the magic of fall into your own kitchen. Enter Greek Yogurt Pumpkin Muffins—a healthier twist on classic pumpkin baking that’s just as cozy and delicious as you’d hope.
These muffins are soft, moist, and filled with warm autumn flavors. Thanks to Greek yogurt, they’re wonderfully tender while sneaking in a little extra protein. The pumpkin puree gives them that dreamy seasonal flavor we all crave (without making them heavy), and a sprinkle of mini chocolate chips takes them from good to “hide-these-from-the-kids” great.
Whether you’re looking for healthy muffins to pop into school lunches, a quick breakfast on busy mornings, or a snack to enjoy with your pumpkin spice latte (because, yes, you can double up on pumpkin), these muffins are the answer. Best part? They only take about 35 minutes from start to finish.
So, grab your mixing bowls, pull out that trusty can of pumpkin, and let’s whip up a batch of muffins that taste like fall wrapped in a hug.
Why You’ll Love These Greek Yogurt Pumpkin Muffins
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Better-for-you treat: Made with Greek yogurt and pumpkin puree for a lighter, protein-packed muffin.
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Quick & easy: Just 10 minutes of prep—perfect for busy mornings.
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Versatile flavors: Keep them simple or mix in chocolate chips or raisins.
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Perfectly cozy: The ultimate fall recipe for breakfast, snacks, or dessert.
Ingredients
(See full measurements above)
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White whole wheat flour (or any wheat flour)
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Sugar
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Baking powder & baking soda
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Salt and cinnamon (or pumpkin spice blend)
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Pumpkin puree (not pumpkin pie filling)
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Egg
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Greek yogurt
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Mini chocolate chips or raisins
Steps to Make Healthy Greek Yogurt Pumpkin Muffins
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Preheat & prep: Heat oven to 350°F. Grease a muffin tin or line with paper liners.
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Mix dry ingredients: In one bowl, whisk flour, sugar, baking powder, baking soda, salt, and cinnamon.
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Mix wet ingredients: In another bowl, stir pumpkin puree, egg, and Greek yogurt until smooth.
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Combine: Gently fold wet into dry until just combined—no overmixing!
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Add extras: Stir in mini chocolate chips or raisins.
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Bake: Divide batter into muffin cups (about ¼ cup each). Bake 22–25 minutes until golden and a toothpick comes out clean.
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Cool & enjoy: Rest 5 minutes in the pan, then move to a wire rack.
Cooking Tips
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Don’t overmix: Stir just until the flour disappears. Overmixing makes muffins tough instead of tender.
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Pumpkin spice swap: Cinnamon works great, but if you’ve got pumpkin spice blend, it takes these muffins up a notch.
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Mix-ins galore: Mini chocolate chips keep things sweet, but walnuts, pecans, or even cranberries would be delicious.
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Moisture check: If you use homemade pumpkin puree, it may be wetter than canned—just blot with a paper towel before using.
A Personal Note from My Kitchen
Pumpkin muffins were one of the first things I baked when my kids were little. They were a hit because they tasted like a treat, but I loved them because they secretly packed in some healthier ingredients. Over the years, I’ve tweaked my recipe—adding Greek yogurt for extra moisture and protein, and sometimes swapping in whole wheat flour for a heartier bite.
These days, they’re our “Sunday afternoon muffins.” We bake a batch together, and by Monday morning, half of them are already gone. My husband claims he’s “helping the kids,” but judging by the chocolate chip smudges, I think we know who sneaks the extras.
What to Serve with Greek Yogurt Pumpkin Muffins
These muffins are versatile enough to shine at any time of day:
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Breakfast on the go: Pair with coffee or a smoothie for a quick start.
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Afternoon snack: Serve with a cup of tea or warm cider.
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Lunchbox treat: Pop one into a school or work lunchbox for a sweet surprise.
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Dessert twist: Warm one up, spread with a little cream cheese frosting, and you’ve got a mini pumpkin cupcake moment.
How to Store
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Room temperature: Store in an airtight container for up to 3 days.
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Fridge: Extend freshness up to 5 days (though they rarely last that long!).
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Freezer: Wrap individually in plastic wrap and freeze for up to 3 months. Defrost at room temperature or warm in the microwave for 20–30 seconds.
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Pro tip: Place a paper towel in the container to absorb excess moisture and keep muffins from getting soggy.
FAQs
Can I make these muffins gluten-free?
Yes! Just swap in a 1:1 gluten-free baking flour.
Do I need to use Greek yogurt, or will regular yogurt work?
Greek yogurt is thicker, which gives these muffins their perfect texture. If you use regular yogurt, reduce it slightly to avoid runny batter.
Can I use pumpkin pie filling instead of pumpkin puree?
Nope—pumpkin pie filling has added sugar and spices. Stick with plain pumpkin puree for the right flavor balance.
How can I make these muffins even healthier?
Try reducing the sugar to ⅓ cup or swapping in coconut sugar or honey. You could also add flaxseed or chia seeds for extra nutrition.
Wrapping It All Up
When it comes to fall recipes, these Greek Yogurt Pumpkin Muffins check all the boxes—they’re cozy, healthy, and downright delicious. Whether you’re baking them for the family, for guests, or just to treat yourself with a warm muffin and a hot drink, they’re the kind of recipe you’ll want to keep on repeat all season long.
So go ahead—embrace the pumpkin craze, pull out your muffin tin, and bake up a batch of muffins that taste like autumn happiness in every bite.
Discover more delicious recipes by following me on Facebook and Pinterest.
Print
Healthy Greek Yogurt Pumpkin Muffins
- Total Time: 35 minutes
- Yield: 12 muffins 1x
- Diet: Low Fat
Description
Healthy Greek Yogurt Pumpkin Muffins are moist, cozy, and packed with fall flavor while being lighter and more nutritious. Made with pumpkin puree and Greek yogurt for extra protein and tenderness, these muffins are perfect for breakfasts, snacks, or lunchbox treats. Mini chocolate chips or raisins add a touch of sweetness, making them a healthy indulgence you’ll bake all season long.
Ingredients
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1 ½ cups white whole wheat flour (or any wheat flour)
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½ cup sugar (adjust to taste)
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1 tsp baking powder
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½ tsp baking soda
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½ tsp salt
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1 tsp ground cinnamon (or pumpkin spice blend)
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1 cup pumpkin puree (not pumpkin pie filling)
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1 large egg
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½ cup Greek yogurt
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½ cup mini chocolate chips or raisins (optional)
Instructions
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Preheat oven to 350°F (175°C). Grease a muffin tin or line with paper liners.
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In a bowl, whisk together flour, sugar, baking powder, baking soda, salt, and cinnamon (or pumpkin spice).
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In another bowl, stir pumpkin puree, egg, and Greek yogurt until smooth.
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Gently fold wet ingredients into dry until just combined—do not overmix.
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Stir in mini chocolate chips or raisins, if using.
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Divide batter into muffin cups, about ¼ cup per muffin.
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Bake 22–25 minutes, until golden and a toothpick inserted comes out clean.
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Cool 5 minutes in the pan, then transfer to a wire rack.
Notes
Don’t overmix; it keeps muffins tender.
Swap cinnamon for pumpkin spice for extra fall flavor.
Add walnuts, pecans, or cranberries for variation.
If using homemade pumpkin puree, blot excess moisture to avoid soggy muffins.
Store with a paper towel in the container to absorb extra moisture.
- Prep Time: 10 minutes
- Cook Time: 22–25 minutes
- Category: Breakfast / Snacks
- Method: Baking
- Cuisine: American