Pumpkin Protein Muffins Recipe
If you’re looking for a cozy and delicious way to power up your mornings or snack time, these Pumpkin Protein Muffins are your new best friend. Rich with autumn spices, packed with wholesome ingredients, and boasting a wonderful balance between healthy nutrition and indulgent flavor, these muffins marry the comforting essence of pumpkin with a protein boost that keeps you energized. Whether you need a quick breakfast on the go or a satisfying post-workout treat, these Pumpkin Protein Muffins deliver on both flavor and nutrition with every bite.

Ingredients You’ll Need
Creating these Pumpkin Protein Muffins is all about combining simple, wholesome ingredients that work harmoniously to give you moist, flavorful, and fluffy muffins with a protein-rich twist. Each component adds its own touch: fragrant spices for warmth, protein powder for nourishment, and pumpkin for moisture and that lovely orange hue.
- Whole wheat pastry flour: Provides a tender crumb and adds a subtle nuttiness while keeping the muffins hearty.
- Protein powder (plain, vanilla, or chocolate): Boosts the nutritional value and complements the pumpkin’s natural sweetness.
- Cinnamon, ground ginger, nutmeg, and cloves: Classic fall spices that create that cozy, comforting flavor profile.
- Baking soda: Essential for helping the muffins rise and become light and fluffy.
- Canned pumpkin puree: Keeps the muffins moist while infusing them with natural sweetness and vibrant color.
- Coconut sugar or brown sugar: Adds gentle sweetness and enhances the spices’ aroma.
- Eggs: Bind everything together and contribute to a soft texture.
- Avocado oil: A healthy fat that helps keep the muffins tender and moist.
- Plain Greek yogurt: Adds creaminess and a slight tang, balancing the sweetness perfectly.
- Vanilla extract: Rounds out the flavors with warm, sweet notes.
- Mini chocolate chips (optional): Little pockets of melty chocolate that take these muffins to the next level.
How to Make Pumpkin Protein Muffins
Step 1: Preheat and Prepare
Start by heating your oven to 375 degrees Fahrenheit and lining a 12-count muffin tin with liners or lightly greasing it. This sets the stage for perfectly shaped muffins with golden edges and a soft interior.
Step 2: Mix Dry Ingredients
In a medium bowl, whisk together the whole wheat pastry flour, your choice of protein powder, warm spices like cinnamon, ginger, nutmeg, and cloves, plus baking soda. This dry mixture is the backbone of your muffins, combining both taste and rise.
Step 3: Combine Wet Ingredients
In a separate large bowl, whisk the pumpkin puree, coconut sugar, eggs, avocado oil, Greek yogurt, and vanilla extract until smooth and creamy. Making sure there are no yogurt clumps ensures a silky batter and an even bake.
Step 4: Bring It All Together
Slowly add the dry ingredient mix to your wet ingredients, stirring gently just until everything comes together. Avoid overmixing to keep the muffins tender. If you love a touch of chocolate, fold in those mini chocolate chips now for delightful bursts of sweetness.
Step 5: Fill, Top, and Bake
Divide the batter evenly into your muffin tin, filling each cup about three-quarters full. Sprinkle a few extra chocolate chips on top if you want a pretty, melty finish. Bake for 20 to 22 minutes or until a toothpick inserted in the center comes out clean. Let them cool before enjoying!
How to Serve Pumpkin Protein Muffins

Garnishes
A dusting of cinnamon or a light smear of cream cheese frosting elevates these muffins for special occasions. You might also enjoy a drizzle of honey or a handful of chopped nuts on top for crunch and extra flavor.
Side Dishes
Serve your Pumpkin Protein Muffins alongside a hot cup of coffee, chai tea, or your favorite smoothie for a perfectly balanced breakfast or snack. Fresh fruit, such as orange slices or berries, complements the spices beautifully and adds a refreshing contrast.
Creative Ways to Present
Turn these muffins into mini desserts by pairing them with a scoop of vanilla yogurt and a sprinkle of granola or toasted coconut flakes. You can also cut them in half, toast lightly, and spread almond butter for an extra protein punch at snack time.
Make Ahead and Storage
Storing Leftovers
Keep your Pumpkin Protein Muffins fresh by storing them in an airtight container at room temperature for up to three days. This keeps them moist and soft without losing their delightful texture.
Freezing
If you want to enjoy these nutritious treats over time, freeze the muffins individually wrapped in plastic wrap or in a freezer-safe bag. They stay delicious for up to two months — perfect for quick breakfasts or snacks when you’re in a hurry.
Reheating
When ready to enjoy, thaw frozen muffins overnight in the fridge or microwave them for about 20-30 seconds until warm. This brings back their freshly baked softness and lets the pumpkin aroma fill your kitchen again.
FAQs
Can I use a different type of flour instead of whole wheat pastry flour?
Absolutely! You can substitute with all-purpose flour for a lighter texture, but whole wheat pastry flour adds a lovely nuttiness and more fiber that complements the pumpkin perfectly.
What protein powder works best for these muffins?
Plain, vanilla, or chocolate protein powder all work wonderfully. Choose a flavor that suits your taste and complements the pumpkin and spices; vanilla is especially popular for its warm, sweet notes.
Are these muffins suitable for freezing?
Yes! Pumpkin Protein Muffins freeze beautifully and thaw well, so you can easily prepare them ahead of time for busy weeks or snack emergencies.
Can I make these muffins dairy-free?
Yes, you can substitute the Greek yogurt with a dairy-free yogurt alternative, and use a non-dairy protein powder to keep the recipe suitable for dairy-free diets without sacrificing flavor or texture.
Do I have to add chocolate chips?
Not at all. The muffins are fantastic on their own with just the pumpkin and spices, but chocolate chips add a lovely burst of sweetness and texture if you want a little indulgence.
Final Thoughts
There’s something truly special about Pumpkin Protein Muffins that makes them feel like a warm hug in muffin form. They’re simple to make, nutritious, and downright delicious—perfect for sharing with family or savoring during those quiet moments at home. Give this recipe a try and watch how these muffins seamlessly blend healthy nourishment with fall-inspired flavor to brighten your day!
PrintPumpkin Protein Muffins Recipe
Delicious and nutritious Pumpkin Protein Muffins made with whole wheat pastry flour, protein powder, warm spices, and creamy pumpkin puree. These muffins are perfect for a healthy breakfast or snack, offering a great boost of protein and seasonal fall flavors.
- Prep Time: 15 minutes
- Cook Time: 20-22 minutes
- Total Time: 35-37 minutes
- Yield: 12 muffins 1x
- Category: Breakfast, Snack, Dessert
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Ingredients
Dry Ingredients
- 1 ¼ cups whole wheat pastry flour
- ½ cup protein powder (plain, vanilla, or chocolate)
- 2 tsp cinnamon
- 1 ½ tsp baking soda
- ½ tsp ground ginger
- ½ tsp ground nutmeg
- ¼ tsp ground cloves
Wet Ingredients
- 15 oz canned pumpkin puree (not pumpkin pie filling)
- ¾ cup coconut sugar or brown sugar
- 2 large eggs
- ¼ cup avocado oil
- ¼ cup plain Greek yogurt
- 2 tsp vanilla extract
Optional
- ½ cup mini chocolate chips (plus extra for topping)
Instructions
- Preheat the oven: Preheat your oven to 375°F (190°C) and line a 12-count muffin tin with paper liners or lightly grease it to prevent sticking.
- Mix dry ingredients: In a medium bowl, whisk together the whole wheat pastry flour, protein powder, cinnamon, baking soda, ground ginger, nutmeg, and cloves. Set the mixture aside.
- Combine wet ingredients: In a separate large bowl, whisk together the canned pumpkin puree, coconut sugar, eggs, avocado oil, plain Greek yogurt, and vanilla extract until smooth and free of yogurt clumps.
- Combine wet and dry: Add the dry ingredient mixture to the wet ingredients. Stir gently until just combined; be careful not to overmix. Fold in the mini chocolate chips if using.
- Fill muffin tin: Evenly divide the batter among the 12 muffin cups. Sprinkle a few mini chocolate chips on top of each muffin for an extra burst of chocolate, if desired.
- Bake: Bake for 20-22 minutes, or until a toothpick inserted in the center of a muffin comes out clean or with just a few moist crumbs.
- Cool and serve: Let the muffins cool in the tin for 5 minutes before transferring to a wire rack to cool completely. Serve warm or at room temperature.
Notes
- For a dairy-free version, substitute Greek yogurt with a non-dairy yogurt alternative.
- Use plain, vanilla, or chocolate protein powder based on your flavor preference.
- If you prefer sweeter muffins, increase the sugar to 1 cup.
- Store muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to a week.
- These muffins freeze well; thaw them at room temperature or warm in the microwave before serving.
- Do not use pumpkin pie filling, as it contains added sugars and spices that will alter the taste and texture.
Nutrition
- Serving Size: 1 muffin
- Calories: 180
- Sugar: 8g
- Sodium: 150mg
- Fat: 7g
- Saturated Fat: 1g
- Unsaturated Fat: 5g
- Trans Fat: 0g
- Carbohydrates: 22g
- Fiber: 3g
- Protein: 8g
- Cholesterol: 40mg
Keywords: pumpkin muffins, protein muffins, healthy muffins, pumpkin protein bake, fall recipes, gluten-conscious snack