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Home » Recipes » Muffins

Pumpkin Protein Muffins with Chocolate Chips

By Laura Fuentes Updated Apr 10, 2026

5 from 11 votes

Recipe

This post may contain affiliate links. Read our disclosure policy here.

Made with oats, Greek yogurt, and your favorite vanilla protein powder, these pumpkin protein muffins are healthy and a breeze to make!

Every bite of these pumpkin protein muffins has chocolate chips for the ultimate treat that’s both irresistible and nutritious.

three pumpkin protein muffins with chocolate chips stacked

Protein Pumpkin Muffins Recipe

These pumpkin protein muffins were a hit with my youngest when he was little and with me because the blender makes this recipe a breeze! Since these muffins are delicious and teens always need added protein, I still make them.

They also love my strawberry yogurt muffins, these pumpkin cottage cheese muffins, and these banana oat muffins (also a blender recipe).

Ingredients

The wet ingredients you’ll need are pumpkin puree, plain or vanilla Greek yogurt (full-fat, 2%, or non-fat), and eggs. The dry ingredients are oats (you’ll blend them, so both old-fashioned rolled oats and quick cooking work), whey or plant-protein vanilla protein powder, pumpkin pie spice, cinnamon, salt, baking powder, and baking soda (it's a denser recipe, so we need both to help the batter rise). Optionally, you can make the muffins extra delicious by adding chocolate chips.

Best Protein Powder for Muffins

I’ve made these protein muffins with whey and plant-based vanilla protein powder. The vanilla flavor sweetens the batter without having to add sugar. When using plant-based powder, the batter might be a bit thicker, yielding denser muffins. If that’s the case, add 2 to 3 tablespoons of water to the batter.

How to Make Pumpkin Protein Muffins

Having made these muffins many times, here are some tips for each step that will give you better results:

  1. Prep the oven.
    Always start with a hot oven. For muffins, I like to position the oven rack in the middle so the heat is distributed evenly. Greasing the pan well is essential for their easy release.
  2. Make the batter.
    I recommend making this batter in a blender so the oats are ground (blended) with the other ingredients to ensure a really smooth batter texture. It's always best to gradually increase the speed so the ingredients incorporate themselves into the batter.
  3. Fill the muffin cups.
    These muffins will rise, so you only need to fill them ¾ of the way to the top. If you're adding chocolate chips to the muffins, add them now. Some will sink others will stay at the top.
  4. Bake the muffins.
    These muffins are quite moist because of the pumpkin puree. I recommend using a toothpick to test that the batter is cooked through around minute 22.
two pumpkin protein muffins with chocolate chips

What Does Protein Pumpkin Muffin Batter Look Like 

The texture of the batter will vary depending on the type of protein you use. Whey protein dissolves great and the batter will be similar to traditional oat muffins. Plant-based proteins tend to be grainier and thicker; therefore, the batter might be a little thicker than you’re used to. Regardless of the protein you use, both turn out great!

More Recipes with Protein Powder

Other favorites you can make with protein powder are these breakfast cookies, in a bowl of protein oatmeal, and even in protein pancakes!

Healthy Pumpkin Protein Muffins (with Oats)

Servings: 12
Prep Time: 10 minutes mins
Cook Time: 25 minutes mins
Total Time: 35 minutes mins
Made with oats, Greek yogurt, and your favorite vanilla protein powder, these pumpkin protein muffins are healthy and a breeze to make!
5 from 11 votes
Print Pin

Ingredients

  • 1 cup pumpkin puree
  • 1 cup Greek yogurt
  • 2 large eggs
  • 1 cup old-fashioned oats, 100g oat flour
  • ½ cup vanilla-flavored protein powder (60g)
  • 2 teaspoons pumpkin pie spice
  • 1 ½ teaspoons cinnamon
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • Pinch salt
  • ½ cup dark chocolate chips, optional

Instructions

Prep:

  • Preheat the oven to 350F and position the oven rack in the middle of the oven. Grease a muffin pan or line it with muffin liners.

Make the batter:

  • Add the ingredients in the order listed inside the blender jar: the pumpkin puree, Greek yogurt, eggs, oats, protein powder, pumpkin spice, cinnamon, baking powder, baking soda, and salt. Blend, increasing the speed from medium to high speed for about 45 seconds, until the ingredients turn into a smooth batter and you can no longer see oat flakes.
  • Pour the batter into the 12 prepared muffin pans, filling them no more than ¾ of the way up. Sprinkle the chocolate chips on top of the muffins.

Bake:

  • Bake the muffins for 22-25 minutes or until a toothpick inserted in the center of a muffin comes out clean. 
  • Remove the pan from the oven and allow the muffins to cool down to room temperature before removing them from the pan.

Serve & store:

  • You can enjoy these muffins warm or at room temperature. 
  • Refrigerate leftover muffins for up to 5 days or freeze them in a zip bag, for up to 2 months. Reheat for 15 to 30 seconds in the microwave.

Notes

  • If using plant-based powder, add 2 to 3 tablespoons of water to the batter, as it may be a bit thicker, yielding denser muffins.

Equipment

¼ cup muffin batter scoop
Muffin Scoop
Clean Treats
Clean Treats Cookbook

Nutrition

Serving: 1 muffin | Calories: 125kcal | Carbohydrates: 12g | Protein: 10g | Fat: 4g | Saturated Fat: 1.5g | Polyunsaturated Fat: 0.3g | Monounsaturated Fat: 0.5g | Trans Fat: 0.003g | Cholesterol: 36mg | Sodium: 114mg | Potassium: 164mg | Fiber: 3g | Sugar: 4g | Vitamin A: 3232IU | Vitamin C: 1mg | Calcium: 93mg | Iron: 1mg

More Muffins

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    Lemon Blueberry Muffins
  • a tray with six pumpkin cottage cheese muffins
    Cottage Cheese Pumpkin Muffins
  • top view of seven Greek yogurt banana muffins
    Greek Yogurt Banana Muffins
  • top view of seven blueberry muffins
    Banana Blueberry Muffins

Comments

    5 from 11 votes (8 ratings without comment)

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    Recipe Rating




  1. Paula Marie says

    December 28, 2025 at 2:52 pm

    5 stars
    Muffins with the same nutrition as an expensive bar with a zillion ingredients? Yes please! And love that they could be made in my vitamix — zero cleanup. Used chocolate whey powder and blended in old fashioned oats (didn’t make a flour first) using gram measurements for everything and they even look pretty – quite the surprise for a blender muffin!

    Reply
  2. Meggan Healy says

    March 21, 2024 at 12:37 pm

    5 stars
    These are so good and so easy to make! My 3-year-old granddaughter helped make them and she LOVED them. The girl all of a sudden doesn’t like anything, so the fact she loves these muffins is HUGE!

    Reply
    • Laura Fuentes says

      March 21, 2024 at 4:35 pm

      Thank you for sharing how much your granddaughter enjoyed these protein muffins!

      Reply
      • Gina says

        November 12, 2024 at 3:42 pm

        5 stars
        Hi Laura, I was wondering if I could swap the Greek yogurt for a vegan coconut yogurt? Thank you for your time

        Reply
        • Laura Fuentes says

          November 15, 2024 at 1:28 pm

          Yes, you can swap it out for a dairy-free yogurt. The texture will change, especially if you’re using an egg replacer and a yogurt replacer.

          Reply
Laura fuentes holding a skillet of food standing in front of a blue door

Hi! I'm Laura.
Certified Integrative Nutrition Health Coach, mom of three, and the woman behind the world’s best pancakes—here to help you ditch the mealtime drama with recipes your family will actually eat.

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