Pumpkin Protein Muffins are studded with semi-sweet chocolate chips and have the perfect spiced pumpkin flavor. These muffins are satiating thanks to the Kodiak protein pancake mix and pumpkin puree. Enjoy one for a quick breakfast, healthy snack, or healthy dessert.

When fall season rolls around, it's time for pumpkin-flavored everything. If the pumpkin craving hits, but you want to reach for something healthier, these protein pumpkin muffins deliver. They have just the right amount of pumpkin flavor with sweet chocolate chips throughout.
The recipe starts with a protein pancake mix. The hearty blend combines with pumpkin puree, egg, and oil to create a moist, tender muffin. Like the double chocolate protein muffins recipe, these muffins come together quickly with simple ingredients.
These tender Kodiak pumpkin muffins are perfect with a cup of coffee or a cold glass of milk. Whether enjoyed for a healthy breakfast or as an afternoon snack, I am sure you will enjoy these chocolate chip pumpkin muffins.
This recipe does not use a whole can of pumpkin puree. If you have extra pumpkin puree, try making a pumpkin cream cheese pie or a tray of these mini pumpkin bread loaves.
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Pumpkin Chocolate Chip Protein Muffins
Muffins are one of the most straightforward baked goods to throw together. The batter is mixed by hand and requires minimal mixing. This protein muffin recipe is easy to make, requires simple ingredients, and bakes in twenty minutes. Here are just a few reasons you will love this simple recipe:
- Easy Muffin Recipe - As stated above, the muffin batter comes together quickly with little effort. The muffins bake fast and can be enjoyed fresh from the oven when the chocolate chips are nice and melty.
- Healthy Breakfast - Each muffin has 6 grams of protein and 3 grams of fiber. Protein pumpkin muffins are great for a quick breakfast, a healthy snack, or a healthy dessert. They provide the perfect fuel you need to get through your day.
- Delicious Muffins - The pumpkin flavor from the puree is emphasized by the pumpkin pie spice in the batter. The healthy pumpkin muffins are perfectly sweet, tender, and delicious - a yummy treat for any time of the year.
Are Protein Muffins Healthy?
These muffins have the added benefit of protein, fiber, and whole grains. All protein pancake mixes are a little different regarding ingredients and ingredient ratios. My favorite brand is Kodiak Cakes. Their mix is made from whole wheat flour with added protein isolates and whey protein.
Not only are you getting the added protein from these muffins, but there are also additional health benefits from the pumpkin puree. Pumpkin is full of antioxidants, vitamin A, and fiber, among many other things.
Ingredients
- Protein Pancake Mix - The brand I use in this recipe is Kodiak Pancake Mix (buttermilk flavor.) These mixes are generally versatile and can be used for other baking purposes like cookies and biscuits.
- Light Brown Sugar (packed)
- Baking Powder
- Salt
- Pumpkin Spice
- Egg (room temperature)
- Pumpkin Puree - As with most baking recipes that require pumpkin, this recipe asks for 100% pumpkin puree, not canned pumpkin pie filling. Pumpkin pie filling has added sugar {and seasonings} which will alter the recipe and the bake.
- Avocado Oil
- Vanilla Extract
- Semi-Sweet Chocolate Chips
See the recipe card for the ingredient quantities.
Ingredient Substitutions
- Light Brown Sugar - Dark Brown Sugar, Granulated Sugar, Stevia, Coconut Sugar
- Avocado Oil - Melted Butter, Coconut Oil, Canola Oil, Vegetable Oil
- Semi-Sweet Chocolate Chips - White Chocolate Chips, Semi-Sweet Chocolate Chunks, Dark Chocolate Chips
Instructions
STEP 1 - Preheat your oven to 375 degrees F. Grease or line the cups of a 12-cup muffin tin and set it aside.
STEP 2 - In a large mixing bowl, whisk together the pancake mix, brown sugar, baking powder, salt, and pumpkin pie spice until thoroughly combined.
STEP 3 - Whisk the avocado oil, egg, and vanilla extract in a small bowl. Pour into the dry ingredients and mix only until combined. Do NOT over-mix. Add the pumpkin puree, again mixing just until combined. The batter may look slightly lumpy or curdled, but this is okay. Stir in the chocolate chips.
STEP 4 - Fill each muffin tin about ¾ the way complete. Bake for 20 to 25 minutes, until golden brown. Allow the muffins to cool before eating.
Variations
- Extra Protein - Mix one tablespoon of vanilla protein powder into the dry ingredients for added protein.
- Eggless - Swap the egg for a flax egg. Mix one tablespoon of ground flaxseed meal with three tablespoons of water. Let it thicken in the refrigerator for 10 minutes before using.
- Gluten-Free - Use gluten-free protein pancake mix, like Kodiak Gluten-Free Protein Pancake Mix or King Arthur Gluten-Free Pancake Mix. Make sure your baking powder is certified gluten-free too.
- Cinnamon - Whisk a ½ teaspoon of ground cinnamon into the dry ingredients in addition to or in place of the pumpkin pie spice.
Serving Suggestions
Pumpkin protein muffins are delicious, warmed, or at room temperature. When warmed, the chocolate chips become melty. Slather muffins with Greek yogurt, almond butter, or peanut butter for additional protein. For extra spiced pumpkin flavor, try the muffins with pumpkin butter.
Delicious Muffin Recipes
- Blueberry Oat Protein Muffins
- Banana Walnut Protein Muffins
- Double Chocolate Protein Muffins
- Peanut Butter Protein Muffins
- Apple Cinnamon Protein Muffins
- Healthy Pumpkin Oatmeal Muffins
Storage
Store the muffins in an airtight container at room temperature for up to 4 days. For a longer shelf life, store them in the refrigerator for up to one week.
Expert Tips
- Refrain from over-mixing the muffin batter to avoid dense, tough muffins. Mix the muffin batter by hand just until it comes together.
- If you do not have paper liners, you can also grease each muffin cup with nonstick spray.
- Bake muffins in a preheated oven for even baking.
Frequently Asked Questions
Transfer cooled muffins to a freezer-safe container or zip-top bag. Freeze the muffins for up to 3 months and thaw them completely before eating.
Kodiak Cakes Power Cakes Mix is readily available at almost every grocery store. When baking, I reach for the classic buttermilk flavor.
If you make the recipe, don’t forget to rate the recipe, and let me know what you think in the comments below! Take pictures, tag #sugarylogic, and share them with me on Instagram or Facebook.
📖 Recipe

Pumpkin Protein Muffins with Chocolate Chips
Equipment
Ingredients
- 2 cups protein pancake mix I used Kodiak Cakes Buttermilk Powercakes Mix.
- ¾ cup light brown sugar packed
- 1 teaspoon baking powder
- ¼ teaspoon salt
- ½ teaspoon pumpkin pie spice
- 1 large egg room temperature
- ¾ cup pumpkin puree
- ¼ cup avocado oil
- 1 cup semi-sweet chocolate chips
- 1 teaspoon vanilla extract
Instructions
- The first step is to preheat your oven to 375° F. Grease or line the cups of a muffin tin and set it aside.
- In a large bowl, whisk together the pancake mix, brown sugar, baking powder, salt, and pumpkin pie spice until thoroughly combined.
- In a small bowl, whisk the avocado oil, egg, and vanilla extract together. Pour into the dry ingredients and mix only until combined. Do NOT over-mix. Add the pumpkin puree, again mixing just until combined. The batter may look slightly lumpy or curdled, but this is okay. Stir in the chocolate chips.
- Fill each muffin tin about ¾ of the way full. Bake for 20 to 25 minutes, until golden brown or until a toothpick inserted into the center comes out clean. Allow muffins to cool before eating.
- Store in an airtight container at room temperature for a few days or in the refrigerator for up to one week.
Nutrition
Did you make this? Leave a review below and tag me on Instagram, Facebook, or Pinterest!
Nourish
These look amazing! Thank you for adding ways to get extra protein in--as vegetarians, that's really important and helpful.
kryan0911
Thank you! These muffins really do pack a punch of protein, and they're delicious too.
thin2win4life
Love this recipe. They look AMAZING!!! I'll be making them this weekend.
kryan0911
Thank you so much! If you do make them, please let me know what you think. 🙂
Liz
I made these today with just a couple swaps. I only had cinnamon oat Kodiak mix which worked great, I used stevia brown sugar and stevia sweetened chocolate chips. I also topped with a few pecans. They were really good. I've made Kodiak muffins before and the key is to not over bake! I will definitely be making these again.
Katelyn Theofanis
Liz, thank you for sharing the modifications you made. I will try adding pecans the next time I make them. I am so happy to hear that you enjoyed these muffins. Thank you for the positive review!