A delightful combination of moist pumpkin puree and a generous dose of high-quality protein powder, creates a healthier treat that satisfies both your sweet tooth and your nutritional needs. These Pumpkin Protein Muffins have a warm, spicy aroma and tender texture that make them the perfect autumn snack or post-workout indulgence.
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Easy Pumpkin Protein Muffins
There’s something about a fluffy and rich muffin that is just so satisfying. And when it’s full of pumpkin pie flavor, but still a nutritious treat, you really can’t resist.
These Pumpkin Protein Muffins are going to become a staple in your fall baking or perhaps all year round. They’re a great breakfast, pre or post workout, or as an afternoon snack.
This muffin recipe uses the entire can of pumpkin, too! One thing that deters me from a lot of pumpkin recipes is they only require ½ cup or so of puree and then i have to figure out what to do with the rest (it usually goes bad sitting in my fridge), but with this recipe you don’t have to worry about that!
Looking for more fall flavor pumpkin treats? Try these Pumpkin Cheesecake Cookies, this Healthier Low Sugar Pumpkin Bread, this Pumpkin Carrot Cake, or these Butterscotch Pumpkin Muffins for something a little more indulgent!
Or if you want other muffin recipes, try these Greek Yogurt Banana Muffins, this Blueberry Protein Muffin Recipe, Oatmeal Raisin Muffins or these One Bowl Double Chocolate Chip Muffins that you'll love, too!
- Eggs - Give our muffins structure and an extra few grams of protein.
- Canned Pumpkin - Use pumpkin purée and not pumpkin pie filling!
- Milk and Greek Yogurt - Make our muffins moist, rich and high protein.
- Whole Wheat Flour - I've not tried alternatives so substitute with caution. Gluten free 1:1 baking flour would definitely work, and I bet oat flour or almond flour would be your next best bets.
- Vanilla Protein Powder - I used Clean Simple Eats Simply Vanilla. Could also use their seasonal Pumpkin Pie Flavor, too. Clean Simple Eats is a whey protein powder and my absolute favorite! Code APOP saves you $$).
- Olive Oil - Could also substitute coconut oil.
- Chocolate Chips - I like dark chocolate chips, but use your favorite!
See the recipe card below for a full list of ingredients and measurements.
Substitutions and Variations
This is such an easy recipe to customize to your liking:
- Swap the chocolate chips for chopped nuts or dried fruit!
- Instead of pumpkin try applesauce or mashed banana.
- You could also substitute the yogurt for cottage cheese for a super rich and moist muffin.
How to Make Protein Muffins
1. Preheat the oven to 350°F. In a large mixing bowl, whisk together eggs, greek yogurt, and canned pumpkin. Whisk until smooth.
2. Whisk in milk and vanilla extract.
3. Add all of the dry ingredients into the bowl except the chocolate chips. Stir until combined (be sure to whisk all of the flour clumps out of the batter).
4. Fold in the olive oil and mini chocolate chips mix until smooth.
5. Place muffin cups into your muffin pan and spray heavily with cooking spray (protein powder is sticky when it bakes. This is a MUST!). Use a 1.5 tbsp cookie scooper and put 2 scoops of muffin batter into each muffin liner. Top each muffin with more chocolate chips before baking.
6. Bake for 25-28 minutes or until a toothpick comes out clean. The tops will brown a bit, this is also due to baking protein powder. Enjoy!
I’ve tested this recipe 3x and here’s what I learned:
- You MUST spray the liners with cooking spray OR use silicone liners. Otherwise half of your muffin will stick to the paper liners
- For best results, whisk in the oil LAST. It keeps the muffins super moist while baking.
- USE a toothpick to see when the muffins are done. They might look like they’re finished baking, but the insides take longer to
These Pumpkin Protein Muffins are FABULOUS for meal prep. Let them cool, then place in an airtight container in the fridge for up to 5 days.
You can also freeze these muffins. Allow them to cool completely then store in a gallon size freezer bag or airtight tupperware for up to 3 months.
Nope, you can leave out the protein powder out of these muffins and use 1 cup of flour total to ensure the proper texture.
Vegan: These muffins have eggs, milk, and yogurt. I’ve not tried it, but I’d bet they’d work with the vegan alternatives - flax eggs, almond milk, and dairy free yogurt. Make sure it’s still a Greek yogurt though, you want the thick texture. Make sure you have a vegan protein powder, too!
Gluten free: You can definitely make this muffin recipe with 1:1 gluten-free baking flour.
More Recipes You'll Love
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Pumpkin Protein Muffins
- Mixing Bowl
- Rubber Spatula
- Measuring cups and spoons
- Muffin tin
- muffin liners
- Cookie scoop
- 2 eggs
- 1 can pumpkin puree
- ¼ cup milk, I used Fairlife Skim
- ⅓ cup plain Greek yogurt, I used Two Good
- 1 tsp vanilla extract
- ½ cup + 2 tbsp whole wheat flour
- ½ cup + 2 tbsp vanilla protein powder, I used Clean Simple Eats
- 1 tsp baking soda
- 1½ tsp baking powder
- ¼ tsp salt
- ½ cup brown sugar
- 1 tsp pumpkin pie spice
- 1 tsp ground cinnamon
- 2 tbsp olive oil
- ½ cup mini chocolate chips
- Preheat the oven to 350°F. In a large mixing bowl, whisk together eggs, greek yogurt, and canned pumpkin. Whisk until smooth.
- Whisk in milk and vanilla extract.
- Add all of the dry ingredients into the bowl except the chocolate chips. Stir until combined (be sure to whisk all of the flour clumps out of the batter).
- Fold in the olive oil and mini chocolate chips mix until smooth.
- Place muffin cups into your muffin pan and spray heavily with cooking spray (protein powder is sticky when it bakes. This is a MUST!). Use a 1.5 tbsp cookie scooper and put 2 scoops of muffin batter into each muffin liner.
- Top each muffin with more chocolate chips before baking.
- Bake for 25-28 minutes or until a toothpick comes out clean. The tops will brown a bit, this is also due to baking protein powder. Enjoy!
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