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Home » Recipes » Muffins

Pumpkin Protein Muffins with Chocolate Chips

By Laura Fuentes Updated Sep 10, 2026

5 from 12 votes

Recipe
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.

overhead view of pumpkin chocolate chip protein muffins on a cooling rack

Protein Pumpkin Muffins Recipe

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

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. Oats (regular or quick) are blended to make oat flour, whey or plant-protein vanilla protein powder, pumpkin pie spice (or cinnamon), salt, baking powder, and baking soda. Chocolate chips are optional but highly recommended!

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 enough without adding sugar, but other flavors, like cinnamon or pumpkin, work great. More in the notes.

How to Make Pumpkin Protein Muffins

  1. Prep.
    Preheat the oven and grease the pan or use parchment liners so the muffins don’t stick. Blend the oats to make oat flour.
  2. Make the batter.
    In a large bowl, combine the wet ingredients. Then add the dry ingredients. Let the batter rest for 10 minutes.
  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.
left: pumpkin protein muffin batter; right: a hand filling a muffin pan qith the batter
  1. Bake.
    For about 22 minutes, until the tops are puffy and a toothpick comes out clean when inserted in the middle.
closeup of pumpkin chocolate chip protein muffins

What Does Protein Pumpkin Muffin Batter Look Like 

The batter is a bit thick but pourable.

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!

Always See My Recipes In Google

Pumpkin Protein Muffins (with Oats)

a hand showing the texture of a pumpkin protein muffin
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 12 votes
Print Pin

Ingredients

  • 2 large eggs
  • 1 cup pumpkin puree
  • 1 cup Greek yogurt, see notes
  • 1 ½ cups old-fashioned oats, or 1 ⅓ cups oat flour
  • ½ cup vanilla-flavored protein powder
  • 1 tablespoon pumpkin pie spice, or 2 teaspoon cinnamon
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • Pinch salt
  • ½ cup 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 parchment muffin liners. If using cupcake liners, spray them.
  • Add the oats to the blender and blend for about 20 seconds until they've turned into oat flour.

Make the batter:

  • In a large bowl, whisk the eggs. Then, add the canned pumpkin puree and Greek yogurt and mix until smooth.
  • Add the protein powder, pumpkin pie spice, baking powder, baking soda, and salt. See note about adding sugar. Mix until smooth.
  • Add the oat flour to the bowl and mix gently until no visible flour remains.
  • Wait 10 minutes for the batter to thicken.
    pumpkin protein muffin batter
  • Pour or scoop ¼ cup of batter into the prepared muffin pan. Distribute the chocolate chips over the muffins, then press them down a little.
    muffin pan with pumpkin protein muffin batter topped with chocolate chips

Bake:

  • Bake the muffins for 22-25 minutes or until the tops are bouncy and a toothpick inserted in the center of a muffin comes out clean. 
    pumpkin protein muffin
  • Remove the pan from the oven and let the muffins cool for 10 minutes before transferring them to a cooling rack.

Store:

  • 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

  • Both whey and plant-based protein powders work with this recipe. The most universal flavor is vanilla, which adds great flavor. Unflavored protein and cinnamon (or similar) flavors work too. 
  • If using plain (unsweetened) Greek yogurt, add 2 tablespoons of plain Greek yogurt and ¼ cup sugar to the recipe. If using a vanilla-flavored Greek yogurt, the sugar can be omitted.
  • Oats, old-fashioned or quick, are blended to make oat flour. You’ll need 1 ½ cups. You can use all-purpose flour or whole-wheat flour for this recipe.
  • Make these gluten-free by using 1 ⅓ cups of a 1:1 all-purpose gluten-free baking mix.
  • Protein amounts per muffin will vary depending on the protein used. Mine has 25g per scoop, adding 60g total to the batter. 

The recommendations below may include affiliate links.

Equipment

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

Nutrition

Serving: 1 muffin | Calories: 124kcal | Carbohydrates: 14g | Protein: 10g | Fat: 5g | Saturated Fat: 2g | Polyunsaturated Fat: 0.4g | Monounsaturated Fat: 1g | Trans Fat: 0.01g | Cholesterol: 38mg | Sodium: 111mg | Potassium: 173mg | Fiber: 2g | Sugar: 4g | Vitamin A: 3223IU | Vitamin C: 1mg | Calcium: 83mg | Iron: 1mg

More Muffins

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    Blender Banana Oat Muffins
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    Chocolate Chip Banana Oat Muffins
  • top view of six mixed berry muffins
    Mixed Berry Muffins
  • top view of lemon blueberry muffins
    Lemon Blueberry Muffins

Comments

    5 from 12 votes (8 ratings without comment)

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    Recipe Rating




  1. Melissa says

    August 19, 2026 at 7:07 pm

    5 stars
    I made a few substitutions using chocolate peanut butter protein (because it’s what I had),added some cocoa powder and vanilla. They taste like healthy brownie bites. I used a mini muffin pan and baked them at 350 for 11 minutes. Absolute perfection!!

    Reply
  2. 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
  3. 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.
Known for the internet’s favorite pancake recipes and real-life dinners that make weeknights easier. These are the meals my family loves, and yours will too!

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