Pumpkin Protein Muffins Recipe
If you are craving a delicious treat that is both nourishing and packed with fall flavors, these Pumpkin Protein Muffins are exactly what you need. They combine the warm spices of pumpkin pie spice with the wholesome goodness of whole wheat flour and the added boost of vanilla protein powder. Perfectly moist and tender, these muffins are a delightful way to enjoy your pumpkin fix while sneaking in some extra protein to keep you energized throughout the day.

Ingredients You’ll Need
Each ingredient in this recipe plays a crucial role, from building flavor and texture to boosting the nutritional profile. Simple yet thoughtfully chosen, these ingredients come together seamlessly to create the perfect muffin experience.
- Whole wheat flour: provides hearty texture and fiber that makes these muffins satisfying.
- Vanilla protein powder: adds a gentle sweetness and muscle-friendly protein without overpowering.
- Pumpkin pie spice: infuses every bite with cozy, aromatic spices like cinnamon, nutmeg, and cloves.
- Baking soda: ensures the muffins rise beautifully and have the ideal crumb.
- Salt: balances the flavors and enhances sweetness.
- Canned pumpkin: delivers that rich, vibrant pumpkin flavor and moisture.
- Milk (or plant-based milk): keeps the batter smooth and tender, perfect for all dietary preferences.
- Greek yogurt: adds creaminess and a slight tang, helping the muffins stay moist longer.
- Avocado oil: supplies healthy fats and a subtle richness without heaviness.
- Honey: natural sweetness that complements pumpkin without being overpowering.
- Vanilla extract: rounds out the flavor profile with its comforting aroma and warmth.
How to Make Pumpkin Protein Muffins
Step 1: Prepare Your Oven and Muffin Tin
Preheat your oven to 350°F (175°C) and get your muffin tin ready by greasing it well or lining it with paper liners. This ensures your muffins come out cleanly and keeps cleanup easy.
Step 2: Mix the Dry Ingredients
In a large bowl, whisk together the whole wheat flour, vanilla protein powder, pumpkin pie spice, baking soda, and salt. This mixes all the leavening and spice evenly into the base of your muffins.
Step 3: Combine the Wet Ingredients
In a separate bowl, blend the canned pumpkin, milk (or milk alternative), Greek yogurt, avocado oil, honey, and vanilla extract until the mixture is smooth and well incorporated. This creates a luscious and rich liquid base that will keep the muffins moist.
Step 4: Gently Fold Wet Into Dry
Pour the wet mixture into the bowl with dry ingredients and fold them together carefully just until everything is combined. Avoid overmixing, which could make the muffins tough instead of tender and fluffy.
Step 5: Fill Muffin Cups
Evenly distribute the batter among the 9 muffin cups, filling each to the top. This helps achieve those perfectly domed, generous muffins everyone’s going to love.
Step 6: Bake Until Perfect
Place your muffin tin in the preheated oven and bake for 30 to 35 minutes, or until a toothpick inserted in the center comes out clean. This baking time gives the muffins enough time to set while keeping them wonderfully moist inside.
Step 7: Cool Before Enjoying
Let the muffins cool in the pan for 10 minutes to firm up, then transfer to a wire rack to finish cooling. This resting time allows the flavors to settle and makes them easier to handle and enjoy.
How to Serve Pumpkin Protein Muffins

Garnishes
Sprinkle your Pumpkin Protein Muffins with a little powdered sugar or cinnamon for a simple, pretty finish. You could also add a dollop of Greek yogurt or a smear of nut butter to each muffin to elevate their flavor before serving.
Side Dishes
Serve these muffins alongside a warm cup of coffee or chai tea for the ultimate cozy pairing. For a more substantial breakfast, add a side of fresh fruit or a small bowl of oatmeal to round out your meal.
Creative Ways to Present
Try slicing the muffins in half and toasting them lightly for a warm and textural twist. You can also turn them into a quick breakfast sandwich by adding cream cheese and sliced apples or bananas, offering a fun and tasty way to enjoy your Pumpkin Protein Muffins.
Make Ahead and Storage
Storing Leftovers
Keep your leftover Pumpkin Protein Muffins in an airtight container at room temperature for up to three days. This helps them stay soft and avoids drying out, perfect for quick breakfasts or snacks on the go.
Freezing
To preserve them longer, wrap individual muffins tightly in plastic wrap and place them in a freezer bag. Frozen Pumpkin Protein Muffins last up to three months and thaw quickly at room temperature or in the microwave.
Reheating
Warm frozen or refrigerated muffins in the microwave for about 20-30 seconds or toast them lightly to revive their fresh-baked charm. Reheating brings back that soft interior and enhances their comforting aroma.
FAQs
Can I substitute the protein powder?
Absolutely! You can swap vanilla protein powder for any flavor you like or use plain protein powder; just expect slight changes in sweetness and flavor. Plant-based protein powders work well too if you prefer vegan options.
Can I use fresh pumpkin instead of canned?
Yes, you can roast and puree fresh pumpkin, but make sure to drain excess moisture so your batter does not become too wet. Using canned pumpkin is simply a convenient shortcut that maintains consistent moisture.
How many muffins does this recipe make?
This recipe yields 9 generously sized Pumpkin Protein Muffins, perfect for a small gathering or a few days of wholesome snacking.
Are these muffins gluten-free?
Since this recipe uses whole wheat flour, it is not gluten-free. To make it gluten-free, substitute a gluten-free flour blend suitable for baking, but note the texture may vary slightly.
Can I add mix-ins like nuts or chocolate chips?
Definitely! Adding walnuts, pecans, or dark chocolate chips can add delightful texture and flavor. Fold them in gently with the wet and dry ingredients to distribute evenly without overmixing.
Final Thoughts
These Pumpkin Protein Muffins are a marvelous balance of wholesome nutrition and comforting flavor, ideal for any pumpkin lover wanting a healthful yet indulgent treat. I truly hope you enjoy making and sharing these as much as I do—there’s nothing quite like a warm muffin fresh out of the oven to brighten your day. Give this recipe a try soon and watch it become one of your favorite go-tos!
PrintPumpkin Protein Muffins Recipe
These Pumpkin Protein Muffins are a wholesome, delicious treat perfect for breakfast or a snack. Packed with whole wheat flour, vanilla protein powder, and nutrient-rich pumpkin, they offer a great balance of protein, fiber, and flavor, enhanced by warm pumpkin pie spice and natural sweetness from honey. Moist and tender, these muffins support a healthy lifestyle with satisfying texture and taste.
- Prep Time: 15 minutes
- Cook Time: 30-35 minutes
- Total Time: 45-50 minutes
- Yield: 9 muffins 1x
- Category: Breakfast, Snack
- Method: Baking
- Cuisine: American
- Diet: Vegetarian
Ingredients
Dry 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
Wet Ingredients
- 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
Instructions
- Preheat Oven: Preheat your oven to 350°F (175°C) and prepare your muffin tins by greasing them thoroughly or lining them with muffin liners to prevent sticking.
- Mix Dry Ingredients: In a large bowl, whisk together the whole wheat flour, vanilla protein powder, pumpkin pie spice, baking soda, and salt until evenly combined and free of lumps.
- Combine Wet Ingredients: In a separate bowl, stir together the canned pumpkin, milk (or non-dairy alternative), Greek yogurt, avocado oil, honey, and vanilla extract until you obtain a smooth, homogeneous mixture.
- Combine Wet and Dry: Gently fold the wet ingredients into the dry ingredients until just combined. Be careful not to overmix to keep the muffins tender and fluffy.
- Fill Muffin Tins: Divide the batter evenly among the 9 muffin cups, filling each to the top for nicely shaped muffins.
- Bake: Place the muffin tin in the oven and bake for 30 to 35 minutes, or until a toothpick inserted in the center of a muffin comes out clean.
- Cool: Allow the muffins to cool in the pan for 10 minutes to set, then transfer them to a wire rack to cool completely before serving or storing.
Notes
- Substitute milk with your choice of almond or oat milk for a dairy-free option.
- Do not overmix the batter to prevent dense muffins.
- Use fresh canned pumpkin puree, not pumpkin pie filling which contains added spices and sugar.
- Store muffins in an airtight container at room temperature for up to 3 days, or refrigerate for up to a week.
- These muffins can be frozen for up to 2 months; thaw before eating.
- Adjust honey for sweetness to taste or substitute with maple syrup.
Nutrition
- Serving Size: 1 muffin
- Calories: 220 kcal
- Sugar: 13 g
- Sodium: 180 mg
- Fat: 8 g
- Saturated Fat: 1 g
- Unsaturated Fat: 6 g
- Trans Fat: 0 g
- Carbohydrates: 29 g
- Fiber: 4 g
- Protein: 9 g
- Cholesterol: 5 mg
Keywords: pumpkin muffins, protein muffins, healthy muffins, whole wheat muffins, pumpkin spice, breakfast muffins, snack recipes, high protein baking

