Ah, Pumpkin Protein Muffins. Just the name alone makes you want to grab a sweater, light a cinnamon-scented candle, and cozy up with a warm cup of coffee, right? If you’re like me—juggling a million things before noon—you know the struggle of finding a healthy fall breakfast that’s both nourishing and grab-and-go friendly. Enter these little beauties: moist, fluffy muffins packed with pumpkin spice goodness and a sneaky dose of protein to keep you energized all morning.

These muffins aren’t just another “healthy snack” that tastes like cardboard. Nope. They’re a feel-good high protein muffin that satisfies both your autumn cravings and your busy schedule. Whether you’re feeding hungry kids, prepping for a hectic workday, or just need a wholesome treat for your coffee break, this recipe has you covered.

Why You’ll Love These Pumpkin Protein Muffins

They’re a healthy fall breakfast that feels like a treat.
Packed with protein to fuel your mornings (or that 3 PM snack attack).
Perfect balance of sweet, spiced, and oh-so-moist.
Freezer-friendly, meal-prep approved.
Optional chocolate chips—because sometimes we deserve a little extra.

Ingredients You’ll Need:

160g whole wheat pastry flour
60g protein powder (plain, vanilla, or chocolate)
2 teaspoons ground cinnamon
1½ teaspoons baking soda
½ teaspoon ground ginger
½ teaspoon ground nutmeg
¼ teaspoon ground cloves
425g canned pumpkin puree (not pumpkin pie filling)
150g coconut sugar or brown sugar
2 large eggs
60ml avocado oil
60g plain Greek yogurt
2 teaspoons vanilla extract
90g mini chocolate chips (optional)

How to Make Pumpkin Protein Muffins:

Preheat & Prep: Preheat your oven to 375°F (190°C). Line a 12-count muffin tin with paper liners.
Mix Dry Ingredients: In a medium bowl, whisk together the flour, protein powder, cinnamon, ginger, nutmeg, cloves, and baking soda. Set aside.
Mix Wet Ingredients: In a large bowl, whisk together the pumpkin puree, coconut sugar, eggs, avocado oil, Greek yogurt, and vanilla extract. Whisk until smooth—no yogurt clumps allowed!
Combine: Gradually fold the dry ingredients into the wet ingredients. Stir gently until just combined. If you’re in the mood, fold in those mini chocolate chips.
Fill & Bake: Divide the batter evenly among the 12 muffin cups. Sprinkle a few extra chocolate chips on top (because… why not?). Bake for 20-22 minutes, or until a toothpick comes out clean.
Cool & Enjoy: Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. Serve and enjoy your high-protein treat!

Olivia’s Pro Tips for Muffin Magic

Protein Powder Tip: A vanilla or chocolate protein powder adds a subtle sweetness, but plain works great too. Just make sure it’s a flavor you enjoy solo.
Don’t Overmix! Stir just until combined to keep the muffins light and fluffy. Overmixing equals dense muffins, and nobody wants that.
Chocolate Chips Are Optional, But Recommended: They add a little indulgence to every bite. If you’re keeping it extra clean, swap with chopped nuts or leave them out.
Test for Doneness: Toothpick testing is your BFF here. If it comes out clean, you’re good to go!

A Little Muffin Story…

You know how some recipes just become part of your family’s DNA? That’s exactly what happened with these Pumpkin Protein Muffins. It all started one chilly October morning when I whipped up a batch for my kids’ soccer practice. I thought they’d be a mom-only snack, but by the time I turned around, half the batch had vanished—tiny chocolatey fingerprints as evidence. Ever since, these muffins are a weekly staple in our house, especially when life gets busy but we still crave a little fall-flavored comfort.

What to Serve with Pumpkin Protein Muffins

These muffins are wonderfully versatile. Pair them with a steaming cup of coffee or a spiced chai latte for the ultimate cozy morning vibe. Need more staying power? Add a dollop of Greek yogurt on the side or a drizzle of almond butter for extra protein. For a balanced brunch spread, serve alongside a fresh fruit salad or a simple scrambled egg dish. And don’t be surprised if they disappear from the table before anything else gets touched!

How to Store Your Muffins (and Keep Them Fresh!)

Once cooled, these Pumpkin Protein Muffins can be stored in an airtight container at room temperature for up to 3 days. If you want them to last longer, pop them in the fridge where they’ll stay fresh for up to a week. They also freeze beautifully! Just wrap each muffin individually in plastic wrap, place them in a freezer-safe bag, and they’ll keep for up to 3 months. When you’re ready to enjoy, a quick zap in the microwave or a slow thaw on the counter will bring them back to life.

FAQs About Pumpkin Protein Muffins

Can I substitute the protein powder?

Absolutely! If you’re out of protein powder, you can swap it with an extra 60g of whole wheat pastry flour. You’ll lose the protein boost, but they’ll still be delicious.

How do I keep my muffins moist?

The pumpkin puree and Greek yogurt work wonders for moisture. Just be careful not to overbake, and store them properly to keep them soft.

Can I make these muffins gluten-free?

Yes! Simply swap the whole wheat pastry flour with your favorite gluten-free baking blend. Just double-check that your protein powder is gluten-free too.

What’s the best way to reheat frozen muffins?

Microwave for about 20-30 seconds or let them thaw at room temperature. They’ll taste freshly baked either way!

If you’ve been searching for a delicious way to sneak some protein into your mornings while indulging in all the cozy feels of fall, these Pumpkin Protein Muffins are your answer. They’re a quick, wholesome fix for busy mornings, afternoon snack cravings, or those “I need pumpkin spice in my life right now” moments. Once you bake them, I promise—they’ll become a permanent guest in your kitchen this season.

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Pumpkin Protein Muffins

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Author: Amanda Thompson
Total Time: 32 minutes
Yield: 12 muffins 1x

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Description

Pumpkin Protein Muffins are the ultimate cozy, high-protein fall breakfast. Moist, fluffy, and packed with warm pumpkin spice flavors, these muffins are a wholesome grab-and-go option that satisfies your autumn cravings while fueling busy mornings. With a sneaky dose of protein and optional chocolate chips, they’re perfect for meal prep, snacks, or a guilt-free treat.

Ingredients

Scale

160g whole wheat pastry flour
60g protein powder (plain, vanilla, or chocolate)
2 teaspoons ground cinnamon
1½ teaspoons baking soda
½ teaspoon ground ginger
½ teaspoon ground nutmeg
¼ teaspoon ground cloves
425g canned pumpkin puree
150g coconut sugar or brown sugar
2 large eggs
60ml avocado oil
60g plain Greek yogurt
2 teaspoons vanilla extract
90g mini chocolate chips (optional)

Cook Mode Prevent your screen from going dark

Instructions

Preheat oven to 375°F (190°C). Line a 12-count muffin tin with paper liners.
In a bowl, whisk together flour, protein powder, cinnamon, ginger, nutmeg, cloves, and baking soda.
In a large bowl, whisk pumpkin puree, sugar, eggs, oil, Greek yogurt, and vanilla until smooth.
Gradually fold the dry ingredients into the wet ingredients until just combined.
Fold in mini chocolate chips if using.
Divide batter evenly among muffin cups. Sprinkle extra chocolate chips on top if desired.
Bake for 20-22 minutes, or until a toothpick inserted in the center comes out clean.
Cool in pan for 5 minutes, then transfer to a wire rack to cool completely.

Notes

Use a flavored protein powder you enjoy, or keep it neutral with plain.

Don’t overmix the batter to keep muffins light and fluffy.

Chocolate chips are optional but add a delightful treat.

Muffins freeze well for up to 3 months; wrap individually for best storage.

For a gluten-free version, substitute with a gluten-free baking blend.

Prep Time: 10 minutes
Cook Time: 22 minutes
Category: Desserts
Method: Baking
Cuisine: American

Pumpkin Protein Muffins: Your Cozy, High-Protein Fall Breakfast Fix