You know those mornings when you’re rushing out the door but still want something warm, cozy, and secretly good for you? That’s exactly why these Greek Yogurt Pumpkin Muffins became my go-to recipe. I stumbled upon this combo one frantic October morning when my kids were begging for pumpkin bread, but I needed something quicker (and let’s be honest, less sugary). The Greek yogurt keeps them crazy moist – like, “how-are-these-so-healthy?” moist – while the pumpkin puree packs in that autumnal hug we all crave. My two little taste-testers gobble them up, and I love that they’re getting protein and fiber without even realizing it. Plus, they come together faster than my coffee brews – total win!

Table of Contents
Table of Contents
Why You’ll Love These Greek Yogurt Pumpkin Muffins
Trust me, these muffins are about to become your new kitchen staple. Here’s why:
- Crazy moist & fluffy – Thanks to Greek yogurt and pumpkin, they stay tender for days (if they last that long!)
- Sneaky-nutritious – Whole wheat flour + protein-packed yogurt = breakfast you can feel good about
- One-bowl easy – Mix, pour, bake – done before the oven finishes preheating
- Kid-approved magic – My picky eaters think they’re getting dessert for breakfast
- Meal prep hero – Freeze a batch and grab one whenever the snack attacks hit
Oh, and that spiced pumpkin aroma? Just try not to eat three straight from the oven – I dare you.
Ingredients for Greek Yogurt Pumpkin Muffins
Grab these simple pantry staples – I bet you’ve got most already! Here’s what makes these muffins shine:
- Dry Team: 1 ½ cups white whole wheat flour (or regular whole wheat), ½ cup sugar, ½ tsp each baking powder & baking soda, ½ tsp salt, ½ tsp cinnamon or pumpkin spice blend
- Wet Wonders: 1 ½ cups pumpkin puree (from a 15-oz can – scoop out 2 Tbsp first!), 1 egg, ½ cup Greek yogurt (that little 5.3oz container is perfect)
- The Fun Part: ½ cup mini chocolate chips or raisins (because life’s too short for boring muffins)
Ingredient Notes & Substitutions
Baking is science, but we can tweak a little! Here’s my tried-and-true swaps:
- Flour: All-purpose works fine if that’s what you’ve got – texture will be slightly lighter
- Sugar: Swap honey or maple syrup (reduce other liquids by 1-2 Tbsp)
- Yogurt: Dairy-free yogurt works, but avoid runny varieties – we need that thickness!
- Egg: Flax egg (1 Tbsp ground flax + 3 Tbsp water) for vegan version
Watch out! Don’t sub applesauce for yogurt – we’ll end up with pumpkin soup instead of muffins. Learned that the hard way!
How to Make Greek Yogurt Pumpkin Muffins
Okay, let’s get baking! These muffins come together so easily – even my five-year-old can help (and believe me, she does!). Here’s how to whip them up:
- Heat things up: Preheat your oven to 350°F (175°C). This is crucial – cold oven = sad, flat muffins.
- Mix the dry team: In a big bowl, whisk together flour, sugar, baking powder, baking soda, salt, and cinnamon. Make sure those leaveners are evenly distributed!
- Whisk the wet crew: In another bowl (or just a measuring cup – I’m all for fewer dishes!), beat the egg, then stir in pumpkin and yogurt until smooth.
- Bring them together: Pour the wet ingredients into the dry mix. Stir just until combined – lumps are totally fine! Fold in chocolate chips or raisins with a gentle hand.
- Fill ’em up: Spoon batter into a greased muffin tin (or lined with sprayed liners) about ⅔ full. I use an ice cream scoop – no mess!
- Bake to perfection: 25 minutes is the sweet spot. They’re done when tops spring back lightly and edges pull away slightly from the pan.

Tips for Perfect Greek Yogurt Pumpkin Muffins
Three golden rules from my many (many) test batches:
- Don’t overmix! Stir until just combined – tough muffins come from overworked batter.
- Spray those liners unless you want half your muffin stuck to the paper (voice of experience here).
- Toothpick test: A few moist crumbs are good; wet batter means they need 2-3 more minutes.
That’s it! Now try not to eat them all before they cool – I won’t judge.
Print
Irresistible Greek Yogurt Pumpkin Muffins in 25 Minutes
Easy and healthy Greek Yogurt Pumpkin Muffins made with whole wheat flour, pumpkin puree, and Greek yogurt. Perfect for breakfast or a snack.
- Total Time: 35 minutes
- Yield: 12 muffins 1x
Ingredients
- 1 ½ cup white whole wheat flour (any wheat flour will work)
- ½ cup sugar
- ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ½ teaspoon ground cinnamon or pumpkin spice blend
- 1 ½ cups pumpkin puree (15-ounce can with 2 Tablespoons removed)
- 1 egg
- ½ cup Greek yogurt (5.3 ounce container)
- ½ cup mini chocolate chips, semi-sweet or raisins
Instructions
- Preheat oven to 350 degrees F.
- Combine flour, sugar, baking powder, baking soda, salt, and cinnamon in a bowl.
- Stir pumpkin, egg, and yogurt into the dry mix.
- Fold in mini chocolate chips.
- Fill muffin tin wells coated with cooking spray about ⅔ full (about ¼ cup of batter). Tip: if using liners, give them a light spritz of cooking spray.
- Bake for about 25 minutes or until the muffins are firm and lightly browned on top.
- Allow muffins to cool for 5 minutes in the pan, then remove to a wire rack to cool further. Enjoy!
Notes
- Store muffins in an airtight container for up to 3 days.
- Freeze muffins for up to 2 months.
- Substitute raisins for chocolate chips if preferred.
- Prep Time: 10 minutes
- Cook Time: 25 minutes
- Category: Breakfast
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Nutrition
- Serving Size: 1 muffin
- Calories: 180
- Sugar: 12g
- Sodium: 220mg
- Fat: 4g
- Saturated Fat: 2g
- Unsaturated Fat: 1g
- Trans Fat: 0g
- Carbohydrates: 32g
- Fiber: 3g
- Protein: 5g
- Cholesterol: 20mg
Storing and Freezing Greek Yogurt Pumpkin Muffins
These muffins actually taste better on day two – the flavors really cozy up together! Keep them fresh by storing in an airtight container at room temp for 3 days. For longer storage, wrap each muffin in plastic wrap, then tuck them into a freezer bag for up to 2 months. To reheat, just pop one in the microwave for 20 seconds (or 30 if frozen) – it’ll taste like it just came out of the oven. I always stash a few in the freezer for those “I-need-a-snack-now” emergencies – my secret mom hack!
Serving Suggestions for Greek Yogurt Pumpkin Muffins
Oh, the possibilities! These muffins are crazy versatile. I love them warm with a smear of almond butter for breakfast, or dunked in my afternoon coffee like a grown-up cookie. Pack them in lunchboxes with some fresh apple slices, or crumble one over Greek yogurt for a parfait situation. Honestly? They’re perfect straight from the tin while standing in the pantry – not that I’d know anything about that. Meal prep dream: bake a double batch Sunday night, and you’ve got grab-and-go goodness all week!
Greek Yogurt Pumpkin Muffins FAQs
I’ve gotten so many great questions about these muffins over the years – here are the ones that pop up most often!
Can I use fresh pumpkin instead of canned?
Absolutely! Roast your pumpkin until super soft, then puree until smooth. Just make sure to drain it well – fresh pumpkin tends to be wetter than canned. I’ll often spread the puree on a towel and let it sit for 15 minutes to remove excess moisture. About 1 ⅔ cups fresh puree equals one can.
How do I make these muffins gluten-free?
Easy fix! Swap the whole wheat flour for your favorite 1:1 gluten-free baking blend. I’ve had great results with Bob’s Red Mill and King Arthur mixes. The texture comes out slightly more delicate, but still wonderfully moist thanks to our Greek yogurt secret weapon.
Why Greek yogurt instead of regular?
Two words: protein and thickness! Greek yogurt adds richness without extra fat, and its tang balances the pumpkin’s sweetness perfectly. Regular yogurt works in a pinch, but you might need to reduce other liquids slightly since it’s thinner. And skip flavored yogurts – we want pure tartness here!
Can I reduce the sugar?
You bet! I’ve successfully cut it to ¼ cup without issues – the pumpkin and chocolate chips (or raisins) add natural sweetness. If you go lower than that, you might want to add a mashed banana or applesauce to keep the muffins tender.
Why do my muffins sink in the middle?
Usually means we got overzealous with mixing! Stop stirring as soon as the flour disappears – those lumps will sort themselves out in the oven. Also double-check your baking powder/soda isn’t expired. And resist opening the oven door until at least the 20-minute mark!
Nutrition Information
These muffins pack a nutritious punch with whole grains, protein, and fiber! Note: Nutrition estimates vary based on specific ingredients and brands used – my kids love them either way.
Did You Make This Recipe?
I’d love to see your Greek Yogurt Pumpkin Muffins! Snap a pic and tag me @FrostyRecipes – nothing makes my day more than seeing your kitchen creations. Happy baking, friends! You can also follow us on Facebook for more delicious recipes.