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Stack of 3 protein pumpkin muffins on a plate. The top muffin has a bite taken out of it. There are more gluten free pumpkin muffins in the background as well as mini pumpkins.

If you love all the flavors of fall, but maybe not all the calories that come with your favorite fall bakes, these healthy pumpkin muffins are for you!

These oat flour muffins are great for breakfast or as a filling snack. As the name suggests, these gluten free muffins are high in protein thanks to whey protein, oats, and Greek yogurt (about 6g of protein per muffin depending on the protein powder used).

Add these yummy pumpkin muffins to your fall baking list today!


Level of difficulty: Easy. Measure, mix, scoop into muffin tins, bake, and enjoy!

Flavor: Pumpkin pie / pumpkin spice

Time: It will take you about 35 minutes to mix up and bake your pumpkin protein muffins

Ingredient shot to make these oat flour pumpkin muffins. This includes: oat flour, cinnamon, salt, baking soda, vanilla whey protein powder, plain greek yogurt, pure maple syrup, pumpkin puree, and eggs.


Canned Pumpkin Puree: using canned pumpkin is a convenient way to bring this fall staple into your home. Pumpkin is a nutrient-dense food, which adds lots of vitamins, minerals, and antioxidants to your protein muffins as well as the pumpkin flavor

Nonfat Greek Yogurt: adds protein and moisture to this easy muffin recipe (without all the fat!)

Pure Maple Syrup: we use just enough maple syrup to add a hint of sweetness to your muffin recipe, without using refined sugar

Large Eggs: eggs add protein and help with the structure and texture

Oat Flour (or Rolled Oats to make your own Oat Flour!): this adds a lot of nutrition to your muffin recipe, and also makes your muffins gluten-free

Vanilla Whey Protein Powder: use a high quality whey protein

Pumpkin Pie Spice: gives this recipe all the pumpkin pie vibes (but without all the calories)

Baking Soda: helps your muffins to rise and give them that muffin texture you’re expecting

Salt: helps to enhance the flavors in this recipe

9 image collage showing the steps for making these healthy pumpkin muffins. Includes mixing of wet ingredients, mixing in dry ingredients, and spooning batter into greased muffin tins.


  1. Mix together wet ingredients: In a large bowl, mix together eggs, yogurt, pumpkin puree, and maple syrup until combined

  2. Add in dry ingredients: add the oat flour, vanilla protein powder, pumpkin pie spice, baking soda, and salt and whisk to combine

  3. Distribute batter into greased muffin tin: spoon muffin batter into a greased muffin tin (or use cupcake liners), filling each cup ¾ of the way full

  4. Bake: bake at 350°F for 23-27 minutes, until browned and a toothpick comes out clean

  5. Cool: allow to cool in the tin for a few minutes then remove the muffins from the tin and place on a cooling rack to finish cooling

  6. Serve and enjoy! Eat as a quick breakfast or snack. Option to add butter or other favorite spread on top!

  7. Store leftovers: store leftover muffins in an airtight container at room temperature or in the fridge for up to 3 days


Making your own oat flour is super easy to do and very inexpensive (I’m always down for a good cost-saving tip!). This is a great option if you do not do a lot of gluten-free baking because you are likely to have regular old-fashioned oatmeal in your cabinets already vs. a special flour.

What is the ratio of rolled oats needed to make oat flour? It is 1-to-1. You will need the same amount of rolled oats / old fashioned oats to make your oat flour as it calls for in your recipe. For instance, if your recipe calls for 1 cup of oat flour, you will need 1 cup of old fashioned oats.

How to make oat flour: Place your rolled oats in a food processor or high-power blender and blend to pulverize. Continue until you’ve reached a flour consistency. You may need to scrape down the sides or bottoms of your processor or blender mid-way through to make sure all the oats are getting blended.

A circular cooling rack with 12 pumpkin protein muffins cooling on it. There is a white napkin next to the cooling rack.


Are you a huge fan of the pumpkin and chocolate combo? Make these into chocolate chip pumpkin muffins by stirring in up to ½ cup of your favorite chocolate chips into the batter. If you do this, I’d recommend holding a few back to sprinkle on top of your muffins after the batter is placed in the muffin tins.


Yes! Freezing muffins is a great option for a quick breakfast or snack at a later date. Below you will find instructions to freeze and reheat frozen muffins.

How to freeze muffins:

  • Cool muffins completely

  • I recommend individually wrapping each muffin in plastic wrap, and storing in a large size ziploc bag. Squeeze out any excess air before storing in the freezer

  • TIP: Write what they are and the date they were baked on the bag for reference

  • TIP: Write reheating instructions right on the bag for easy eating

How to reheat frozen muffins:

  • To reheat from frozen: unwrap individual muffins and place on a microwave safe plate (optionally lined with a paper towel). Microwave for approximately 30 seconds.

  • Thaw at room temperature: if you have more time, you can also thaw your muffins at room temperature. Remove the number of individually wrapped muffins you would like from the freezer and place on your countertop. Muffins will be thawed in about 1-2 hours.

How long can you freeze muffins for?

  • Frozen muffins will keep in a standard freezer for 2-3 months after they are baked

Close up of a stack of 3 healthy pumpkin muffins. There are additional oat flour muffins in the background, as well as mini pumpkins, a whey protein container, and a can of pumpkin puree.


Is this a gluten free protein muffins recipe? Yes. However, please check your rolled oats or oat flour to make sure the label specifically notes that it is gluten free. Oatmeal can be cross-contaminated depending on where it is processed. It is also good practice to double-check that your protein powder does not contain gluten.

Can I make this into a vegan protein muffins recipe? Yes. Substitute the eggs with flax eggs, use a vegan-friendly yogurt, and select a vegan-friendly protein powder in lieu of whey protein. Please note, I have not made these substitutions myself. Doing so may affect the texture of these muffins.

What’s the best protein powder to use in this recipe? My personal favorite is Simply Tera’s because it has minimal ingredients (4 total!) and it tastes great. If you are looking to make this into a vegan snack recipe, select a plant-based protein powder like this one.


*Disclosure: This post contains affiliate links, which means at no additional cost to you I may receive a small commission for purchases made through these links. However, please know that I only provide links to products that I actually use and wholeheartedly recommend!