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Home » Recipes » Muffins & Scones

Pumpkin Protein Muffins with Chocolate Chips

By Laura Fuentes Updated Mar 27, 2025

5 from 10 votes

Recipe

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

Oh! And the chocolate chips in every bite make these pumpkin protein muffins irresistible.

protein muffins

Protein Pumpkin Muffins Recipe

When my kids were little, I nearly always had some type of healthy muffin on hand for their morning breakfast or snack -either at home or packed for school. These pumpkin muffins with protein were a hit with my son and with me because the blender makes this recipe a breeze!

Years later, I still make them because they’re delicious and the added protein is something teens need more of in their day! Other muffins they love are these strawberry yogurt muffins, these chocolate zucchini muffins, and these healthy banana oat muffins -also a blender recipe.

Ingredients

You’ll find the amounts to these pumpkin protein muffins in the recipe card; but before you go make any swaps or substitutions, check out which ones I’ve already tested in this list:

  • Oats: old-fashioned rolled oats or quick cooking will work for this recipe.
  • Pumpkin: canned pumpkin puree or homemade.
  • Greek yogurt: the thicker texture of the yogurt adds protein and volume in this recipe. Use full-fat, 2%, or non-fat Greek yogurt, plain or vanilla.
  • Eggs: used to bind the recipe. I’ve made these muffins with an egg replacer, and the texture is slightly different, but they do hold up.
  • Vanilla protein powder:  I’ve found that vanilla sweetens this recipe; use whey or plant-protein powder.
  • Pumpkin pie spice: all the flavors of fall in a little bit of spice.
  • Cinnamon: balances out the spice.
  • Baking powder: helps these muffins rise.
  • Baking soda: since it’s a denser recipe, we’re adding baking soda to help the baking powder lift.
  • Salt: to enhance the flavors of the muffins.
  • Chocolate chips: optional in the recipe but a delicious find in every bite.

How to Make Pumpkin Protein Muffins

Making these is similar to making traditional muffins. Having made these many times, here are some tips in each step that will give you better results:

  1. Prep
    Always start with a hot oven. For muffins, I like to position the oven rack, where the tray will sit, in the middle of the oven 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
    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.
  5. Cool
    Let the muffins cool down in the muffin pan before removing them. You can enjoy them warm or at room temperature. 
  6. Storage
    These protein muffins will last a week in the fridge and freeze great!

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, they should both turn out great!

How to Know Protein Muffins are Done

I use the old-school method to see if my muffins are done and that’s what I’d recommend too! Insert a toothpick at the highest point and middle of the muffin around minute 22. It should come out clean, not wet with batter. If so, continue baking for another 3 minutes and test a different muffin.

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.

protein muffins

More Recipes with Protein Powder

Protein powder is really versatile and it’s a great way to add more nutrition to recipes my family already loves. Other favorites 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
Made with oats, Greek yogurt, pumpkin puree, and your favorite vanilla protein powder, these pumpkin protein muffins are healthy and a breeze to make!
5 from 10 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.

Storage:

  • 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.

Equipment

Clean Treats
Clean Treats Cookbook
Muffin Pan

Nutrition

Serving: 1serving | 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

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Comments

    5 from 10 votes (8 ratings without comment)

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    Recipe Rating




  1. 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

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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