Name: Pumpkin Protein Muffins
Prep time: 10 min
Cook time: PT-489793H26M44S
Total time: 50 min
Cuisine: American
Ingredients: 1.5 cups (180 g) whole wheat flour; ½ cup (40 g) vanilla protein powder; 1.5 tbsp (12 g) pumpkin pie spice; ½ tsp (2.5 g) baking soda; ½ tsp (2.5 g) salt; 15 oz (425 g) canned pumpkin; ¼ cup (60 ml) milk (or almond/oat milk); ½ cup (120 g) Greek yogurt; ¼ cup (60 ml) avocado oil; ½ cup (120 ml) honey; 1 tsp (5 ml) vanilla extract

Jump to Recipe

When the weather cools down and the leaves crunch underfoot, there’s one thing I can’t resist—pumpkin everything. These pumpkin protein muffins are a little hug in muffin form: moist, flavorful, and secretly packed with wholesome ingredients that make them just as good for you as they are delicious. Think of them as the happy marriage between comfort food and healthy living—a balance we’re all striving for, right?

If you’ve ever wanted a fall treat you can enjoy without that sugar crash an hour later, these muffins are your answer. They’re rich in protein, made with whole wheat flour, Greek yogurt, and just the right amount of natural sweetness from honey. Whether you need a grab-and-go breakfast, a lunchbox filler, or a guilt-free afternoon snack with coffee, these muffins will quickly become a household favorite. And bonus—they make your kitchen smell like pumpkin spice heaven.

So, tie on that apron, friend. We’re about to bake up some cozy comfort that’s as nourishing as it is tasty.

Why You’ll Love These Pumpkin Protein Muffins

They’re packed with protein and fiber, keeping you fuller for longer.
The flavor? Like a warm slice of pumpkin pie but in a muffin you can eat on the go.
Kid-approved and freezer-friendly.
No refined sugar crash—just real, wholesome sweetness.

Ingredients You’ll Need

1.5 cups (180 g) whole wheat flour
½ cup (40 g) vanilla protein powder
1.5 tablespoons (12 g) pumpkin pie spice
½ teaspoon (2.5 g) baking soda
½ teaspoon (2.5 g) salt
15 oz (425 g) canned pumpkin
¼ cup (60 ml) milk
½ cup (120 g) Greek yogurt
¼ cup (60 ml) avocado oil
½ cup (120 ml) honey
1 teaspoon (5 ml) vanilla extract

How to Make Pumpkin Protein Muffins

Preheat your oven to 350°F (175°C). Line or grease 9 muffin tins.
In a large mixing bowl, whisk together flour, protein powder, pumpkin pie spice, baking soda, and salt.
In another bowl, stir together canned pumpkin, milk, Greek yogurt, avocado oil, honey, and vanilla until smooth.
Make a little well in the dry ingredients, then fold in the wet ingredients. Mix gently—overmixing makes tough muffins.
Spoon the batter into the muffin tins, filling each one to the top.
Bake for 30–35 minutes, or until a toothpick comes out clean.
Let them cool for 10 minutes in the pan, then transfer to a rack.

Tips for Perfect Healthy Pumpkin Muffins

Use room-temperature Greek yogurt—it mixes more smoothly.
If your protein powder is sweetened, you may want to slightly reduce the honey.
Don’t skip the cooling step. Muffins finish setting as they cool, so patience pays off.
For extra texture, toss in a handful of chopped walnuts or dark chocolate chips.
Want them extra moist? Swap milk for almond milk or oat milk—it adds a subtle nutty flavor.

And don’t worry if your batter looks thick—that’s normal for whole wheat pumpkin muffins. The result is tender, hearty goodness.

A Little Story from My Kitchen

These muffins started as a “happy accident.” One fall morning, I was testing a new recipe for pumpkin bread, but I was out of white flour. In true “use what you’ve got” fashion, I grabbed the whole wheat flour, added some protein powder I had in the pantry, and voilà—something magical happened.

My husband, who is usually the “just give me eggs and toast” kind of breakfast guy, couldn’t stop raving about them. And my kids? They thought they were cupcakes and begged for more. Since then, these pumpkin muffins with yogurt have become a staple in our house every fall—perfect for breakfast, snacks, or sneaking into lunchboxes with a little note.

Food has this beautiful way of becoming part of our traditions, and now these muffins feel like a little piece of our family’s autumn story.

What to Serve with Pumpkin Protein Muffins

These muffins are versatile little gems. For breakfast, pair them with a latte or a hot cup of chai for the ultimate cozy start. If you’re in need of a post-workout refuel, enjoy one with a protein smoothie or even a little smear of almond butter for extra staying power.

Hosting brunch? Serve them alongside a fruit salad and scrambled eggs—they balance sweet and savory beautifully. And don’t underestimate them as dessert! Warm one up, add a dollop of whipped cream (or Greek yogurt if you’re feeling virtuous), and you’ve got yourself a fall-inspired treat worthy of any gathering.

Basically, they’re good anytime, anywhere—coffee in hand highly recommended.

How to Store Pumpkin Muffins

Room temperature: Keep in an airtight container for up to 3 days. They stay moist and flavorful.
Fridge: Store for up to a week. Just warm in the microwave for 10–15 seconds before eating.
Freezer: Wrap individually in plastic wrap and store in a freezer bag for up to 3 months. Defrost overnight in the fridge or zap for 30 seconds in the microwave.

Pro tip: Freeze half your batch so you can enjoy fresh muffins now and still have a little stash ready when that pumpkin craving strikes.

FAQs About Pumpkin Protein Muffins

Can I substitute the flour?

Yes! You can swap whole wheat flour for all-purpose flour or a gluten-free blend. The texture may be slightly lighter with all-purpose.

Can I make these muffins dairy-free?

Absolutely. Use a dairy-free yogurt and plant-based milk. The recipe holds up beautifully.

Do I need protein powder?

Nope. If you don’t have it, just replace it with more flour. They’ll still taste amazing, just with a little less protein.

How do I make them sweeter?

Add 2–3 tablespoons of brown sugar or maple syrup. They’re mildly sweet as written.

Can I add mix-ins?

Yes! Dark chocolate chips, pecans, or dried cranberries all work wonderfully.

Bake Up Cozy Joy

There’s something about pumpkin protein muffins that makes life just a little sweeter—and a little healthier. They’re the kind of recipe that fits into your busy weekday mornings, yet also feels special enough to share on a lazy Sunday with family. Every bite is a mix of cozy pumpkin spice and nourishing ingredients, reminding us that comfort food doesn’t have to come with guilt.

So go ahead, preheat that oven and fill your kitchen with the smell of fall. These muffins aren’t just a recipe—they’re a memory waiting to be made.

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