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Healthy Pumpkin Protein Muffins

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These healthy pumpkin protein muffins are soft, moist, and packed with pumpkin flavor and protein. They come together with simple ingredients, freeze beautifully, and are perfect for breakfast, a snack, lunch boxes, or packing for a trip.

Healthy Pumpkin Protein Muffin on a white liner with pumpkin seeds around

“Healthy” can mean something different to everyone, but these muffins use several simple ingredients I love incorporating into everyday baking. Rather than traditional all-purpose flour, we blend rolled oats into oat flour. Pumpkin purée provides moisture and natural sweetness, and vanilla whey protein adds extra protein.

Looking for more fall baking? Try my…Chewy Pumpkin Chocolate Chip Cookies. Gluten-Free Oatmeal Apple Muffins, and Pumpkin Muffins with Oats.

Why You’ll Love These Muffins

  • Wholesome & hearty – Oats give them a satisfying texture without being heavy.
  • Extra protein from vanilla whey protein powder.
  • Quick & easy – Two bowls, simple ingredients, ready in under 30 minutes.
  • Freezer-friendly – Bake once, enjoy all week.
Healthy Pumpkin Protein Muffins in an orange bowl

Ingredients at a Glance

Oats – Blended into flour for a hearty, wholesome base. Old-fashioned rolled oats work best.

Pumpkin purée – Use plain canned pumpkin purée, not pumpkin pie filling, or make your own.

Vanilla whey protein powder – Adds protein and a subtle vanilla flavor. Since protein powders vary, texture can vary slightly by brand.

Unsweetened milk – Use whatever unsweetened milk you have on hand: almond, dairy, oat, or another milk.

Eggs – For structure.

Vanilla extract and pumpkin spice – Bring the classic fall flavors together.

How to Make Pumpkin Puree

Skip the can if you want! Here’s how:

  1. Peel a small sugar pumpkin and cut it into 1-inch cubes.
  2. Place cubes in a pot with about ½ cup of water.
  3. Bring to a boil, then reduce the heat and simmer for 15–20 minutes until very tender.
  4. Drain well, let it cool, and blend until smooth (or mash with a potato masher).

Tips for the Best Muffins

  • Use pumpkin purée, not pumpkin pie filling: Purée is just pumpkin; pie filling already has sugar and spices added.
  • Don’t overmix the batter: Stop once the wet and dry ingredients are combined; overmixing makes denser muffins.
  • Don’t overbake: These should be moist and tender; start checking at the 18-minute mark.
Healthy Pumpkin Protein Muffin with pumpkin seeds around

FAQs

How do I store Pumpkin Muffins?

Store in an airtight container for up to 3-4 days.
Freezer-friendly: Once completely cooled, place in a freezer-safe bag or container. They’ll keep well for up to 3 months. To enjoy later, thaw at room temp or microwave for 20–30 seconds.

How do I know when they’re done?

The tops should be lightly golden and bounce back when gently pressed.
A toothpick inserted in the center should come out clean or with just a few moist crumbs—no wet batter.

Can I make these without protein powder?

You can experiment with leaving it out (I haven’t tried it myself), but expect a different texture, and you may need to adjust the dry ingredients.

What kind of pumpkin purée should I use?

Use 100% pure pumpkin purée without any add-ons, not pumpkin pie filling.

Original recipe by “Healthy Kitchen.”

Healthy Pumpkin Protein Muffins

These healthy pumpkin protein muffins are soft, moist, and packed with pumpkin flavor and protein.
Prep Time10 minutes
Cook Time20 minutes
Servings: 10 muffins
Author: Rachel

Ingredients

For the muffins:

  • 2 cups rolled oats
  • 1/2 cup vanilla protein powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • a pinch of salt
  • 1 teaspoon pumpkin pie spice or cinnamon or a combination
  • cups pumpkin purée
  • 2 large eggs
  • 1/4 cup coconut sugar or light brown sugar
  • 1/3 cup unsweetened milk of choice
  • 1 teaspoon vanilla extract
  • Cooking spray

For the topping (optional):

  • 1/4 cup pumpkin seeds
  • 1/4 cup coconut sugar or light brown sugar
  • 1/4 teaspoon pumpkin pie spice or cinnamon or a combination

Instructions

  • Preheat the oven to 350°F/180°C. Line a muffin pan with paper liners and lightly spray with cooking spray.
  • Blend the rolled oats until fine and flour-like.
  • In a large bowl, whisk together the oat flour, protein powder, baking soda, baking powder, salt, and pumpkin pie spice and/or cinnamon.
  • In a separate bowl, whisk the pumpkin purée, eggs, sugar, milk, and vanilla extract until smooth.
  • Add wet ingredients to dry and stir until just combined.
  • Divide batter evenly among the 10 muffin cups, filling each to the top.
  • Mix pumpkin seeds, sugar, and pumpkin pie spice and/or cinnamon; sprinkle over muffins, gently pressing seeds into the batter.
  • Bake 18–20 minutes, until a toothpick inserted into the center comes out clean.
  • Cool in the pan a few minutes, then transfer to a wire rack to cool completely.
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