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

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
- 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. - Make the batter.
In a large bowl, combine the wet ingredients. Then add the dry ingredients. Let the batter rest for 10 minutes. - 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.

- Bake.
For about 22 minutes, until the tops are puffy and a toothpick comes out clean when inserted in the middle.

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!
Pumpkin Protein Muffins (with Oats)

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.
- 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.
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.
- 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.
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Melissa says
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!!
Paula Marie says
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!
Meggan Healy says
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!
Laura Fuentes says
Thank you for sharing how much your granddaughter enjoyed these protein muffins!
Gina says
Hi Laura, I was wondering if I could swap the Greek yogurt for a vegan coconut yogurt? Thank you for your time
Laura Fuentes says
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.