Protein Muffins – Pumpkin Spice Comfort with a Healthy Twist
Pumpkin spice season doesn’t have to mean sugary coffee drinks and heavy desserts. These Protein Muffins bring cozy fall flavor with a balanced, feel-good boost. They’re soft, lightly sweet, and perfect for breakfast, a snack, or a post-workout bite.
You get the pumpkin pie vibes without the crash. Plus, they’re easy to make with pantry staples and come together in one bowl.

Ingredients
Method
- Prep your pan and oven: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with liners or lightly grease it.
- Whisk the wet ingredients: In a large bowl, whisk pumpkin puree, eggs, Greek yogurt, maple syrup, oil, and vanilla until smooth.
- Blend or pulse the oats (optional): For a softer crumb, pulse the oats a few times in a blender. Leave them whole if you want more texture.
- Combine the dry ingredients: In a separate bowl, stir together oats, flour, protein powder, pumpkin pie spice, baking powder, baking soda, and salt.
- Bring it together: Add the dry mixture to the wet ingredients. Stir gently until just combined. Avoid overmixing to keep muffins tender.
- Fold in extras: If using chocolate chips, nuts, or pepitas, fold them in. The batter will be thick—that’s normal.
- Fill the tin: Divide the batter evenly among the muffin cups, filling each about 3/4 full.
- Bake: Bake for 17–22 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs.
- Cool: Let muffins cool in the pan for 5 minutes, then transfer to a wire rack. Cooling helps them set and improves texture.
- Enjoy: Serve warm or at room temperature. A swipe of almond butter on top is excellent.
What Makes This Special

These muffins deliver the familiar warmth of pumpkin spice while packing real staying power. Pumpkin puree adds moisture and natural sweetness, so you don’t need much sugar.
Protein powder helps each muffin feel more satisfying, and oats bring fiber and texture. The result is a tender, bakery-style muffin that supports your goals without tasting “healthy.” Key highlights:
- Balanced macros: Protein, fiber, and smart carbs for steady energy.
- No dry crumble: Pumpkin keeps the crumb moist and soft.
- Easy swaps: Dairy-free, gluten-free, or nut-free adjustments are simple.
- Meal-prep friendly: Freezes well and reheats beautifully.
Ingredients
- 1 cup pumpkin puree (not pumpkin pie filling)
- 2 large eggs (room temperature if possible)
- 1/2 cup plain Greek yogurt (or dairy-free yogurt)
- 1/3 cup pure maple syrup or honey
- 2 tablespoons avocado oil or melted coconut oil
- 1 teaspoon vanilla extract
- 1 cup rolled oats (quick oats also work)
- 3/4 cup white whole wheat flour or oat flour
- 1/2 cup vanilla or unflavored whey or plant-based protein powder
- 2 teaspoons pumpkin pie spice (or 1.5 tsp cinnamon, 1/4 tsp nutmeg, 1/4 tsp ginger, pinch cloves)
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/4 teaspoon fine sea salt
- Optional mix-ins: 1/3 cup mini chocolate chips, chopped pecans, or pepitas
Step-by-Step Instructions

- Prep your pan and oven: Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with liners or lightly grease it.
- Whisk the wet ingredients: In a large bowl, whisk pumpkin puree, eggs, Greek yogurt, maple syrup, oil, and vanilla until smooth.
- Blend or pulse the oats (optional): For a softer crumb, pulse the oats a few times in a blender.
Leave them whole if you want more texture.
- Combine the dry ingredients: In a separate bowl, stir together oats, flour, protein powder, pumpkin pie spice, baking powder, baking soda, and salt.
- Bring it together: Add the dry mixture to the wet ingredients. Stir gently until just combined. Avoid overmixing to keep muffins tender.
- Fold in extras: If using chocolate chips, nuts, or pepitas, fold them in.
The batter will be thick—that’s normal.
- Fill the tin: Divide the batter evenly among the muffin cups, filling each about 3/4 full.
- Bake: Bake for 17–22 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs.
- Cool: Let muffins cool in the pan for 5 minutes, then transfer to a wire rack. Cooling helps them set and improves texture.
- Enjoy: Serve warm or at room temperature. A swipe of almond butter on top is excellent.
Keeping It Fresh
These muffins keep well and are great for meal prep.
Store them in an airtight container at room temperature for 1–2 days. If your kitchen is warm, refrigerate for up to 5 days. Freezing tips:
- Cool completely before freezing.
- Wrap each muffin individually or place them in a single layer in a freezer bag.
- Freeze for up to 3 months. Reheat in the microwave for 25–35 seconds or warm in a 300°F (150°C) oven for 8–10 minutes.

Why This is Good for You
These muffins bring more than taste.
Pumpkin is rich in beta-carotene, which supports eye and immune health. Oats add soluble fiber that can help with steady digestion and fullness. Protein powder helps maintain and repair muscle, and when combined with carbs, it supports recovery after exercise. Smart balance:
- Protein: Supports satiety and muscle repair.
- Fiber: Aids digestion and helps keep you full.
- Moderate sugar: Maple syrup sweetens without overwhelming the recipe.
Pitfalls to Watch Out For
- Overmixing the batter: This can make muffins tough.
Mix just until the dry streaks disappear.
- Using the wrong pumpkin: Pumpkin pie filling contains sugar and spices. Use pure pumpkin puree.
- Too much protein powder: Adding extra can make the muffins dry. Stick to the amount listed.
- Skipping fat: A little oil keeps the crumb tender.
Don’t omit it entirely.
- Baking too long: Protein muffins dry out faster. Start checking at 17 minutes.
Variations You Can Try
- Dairy-free: Use a dairy-free yogurt and plant-based protein powder. Coconut oil works well for the fat.
- Gluten-free: Choose certified gluten-free oats and use oat flour or a 1:1 gluten-free flour blend.
- Low-sugar: Reduce maple syrup to 1/4 cup and add 2 tablespoons unsweetened applesauce for moisture.
- Coffeehouse twist: Stir 1 teaspoon instant espresso into the dry ingredients for a pumpkin latte vibe.
- Crunch top: Sprinkle turbinado sugar and pepitas on top before baking for a lightly crisp finish.
- Chocolate lovers: Use mini dark chocolate chips and a chocolate protein powder for a mocha-pumpkin flavor.
- Spice-forward: Add extra cinnamon or a pinch of cardamom for deeper warmth.
FAQ
Can I use almond flour instead of wheat or oat flour?
Almond flour behaves differently and can make the muffins too moist and dense.
If you want to use it, replace only half the flour with almond flour and add an extra tablespoon of oat flour to help bind.
Which protein powder works best?
Whey protein blends tend to create a softer crumb. Plant-based powders work too, but can absorb more moisture, so you may need 1–2 extra tablespoons of yogurt or a splash of milk to keep the batter from getting dry.
Can I make these without eggs?
Yes. Use two flax eggs (2 tablespoons ground flaxseed mixed with 5 tablespoons warm water; rest 5 minutes).
The texture will be slightly denser but still moist and tasty.
How do I know when they’re done?
Look for set tops that spring back lightly when pressed. A toothpick should come out mostly clean with a few moist crumbs. If it’s wet, bake for 1–2 more minutes and check again.
Do I need muffin liners?
Liners make cleanup easier and help prevent sticking, especially with high-protein batters.
If you skip liners, grease the tin well and let muffins cool 10 minutes before removing.
Can I reduce the oil?
You can cut the oil to 1 tablespoon and add 1 extra tablespoon of Greek yogurt. The muffins will be a bit less tender but still good.
What’s the best way to reheat?
Microwave a muffin for 20–30 seconds, or split and toast lightly. If frozen, thaw overnight in the fridge or reheat from frozen for 30–45 seconds.
In Conclusion
Protein Muffins with Pumpkin Spice bring comfort and nourishment together in one small package.
They’re simple to make, easy to customize, and ideal for busy mornings or steady afternoon energy. Keep a batch on hand, and you’ll have a cozy, satisfying bite ready whenever you need it. Warm, spiced, and packed with protein—this is fall baking that supports the way you live.
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