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    Home » Breakfast

    Pumpkin Protein Muffins

    Published: Oct 3, 2021 · Modified: Sep 4, 2022 by Samantha Ensinger · 11 Comments

    Jump to Recipe Print Recipe
    a stack of pumpkin muffins

    These pumpkin protein muffins have a delicious cinnamon sugar topping that make them absolutely delicious. Made with pure pumpkin, greek yogurt, and NO protein powder, these muffins are healthy and perfect for fall.

    a pumpkin muffin with cinnamon sugar topping

    These pumpkin protein muffins are a quick and easy recipe to make for Halloween, Thanksgiving, and your favorite fall events. They have such a fluffy texture that everyone is sure to enjoy.

    This recipe was inspired by my vegan pumpkin banana bread, and pairs well with this pumpkin spice iced latte. Give me all the fall things, right!?

    Jump to:
    • Ingredients for Pumpkin Muffins
    • How to Make Pumpkin Muffins
    • Gluten-Free, Vegan Pumpkin Muffins
    • Variations to the Muffins
    • Storing the Muffins
    • More Recipes To Enjoy
    • Recipe
    • Pumpkin Protein Muffins

    Ingredients for Pumpkin Muffins

    You can rest assured knowing all the ingredients for these pumpkin protein muffins are healthy and good for you. This recipe is refined-sugar free and full of whole grains.

    ingredients to make the pumpkin muffins
    • whole wheat pastry flour: this whole wheat flour is made from a soft wheat that has a light and mild taste in addition to great nutritional benefits.
    • ground flax seed: flax seed packs plenty of fiber, protein, and Omega 3s into these muffins and acts as a second flour in the recipe.
    • pumpkin pie spice & cinnamon: these spices add the best fall flavors to the muffins!
    • baking soda: this helps the muffins rise properly and gives them a springy, fluffy texture
    • salt: adding salt balances the flavors and enhances the sweetness of the muffins.
    • eggs: eggs add structure to the muffins and keeps them moist.
    • 100% pure pumpkin puree: pure pumpkin is very heatlhy for you and gives these muffins that signature fall flavor!
    • vanilla greek yogurt: this is the main protein source in the muffins. I like to use a vanilla greek yogurt for optimal results and flavor.
    • unsweetened applesauce: this provides additional sweetness to the muffins. For even sweeter muffins, use a sweetened applesauce instead.
    • coconut oil: this adds moisture to the muffins and keeps them from becoming dry!
    • pure vanilla extract: vanilla enhances all the flavors in the recipe.

    For the cinnamon sugar topping, you just need a couple ingredients.

    • coconut sugar: this is an unrefined sugar that has more vitamins and minerals than traditional cane sugar.
    • ground cinnamon: adds to those delicious fall flavors!

    How to Make Pumpkin Muffins

    I'm not kidding when I say these pumpkin muffins are so easy to make. The batter takes less than 15 minutes to prepare!

    STEP 1: Prepare oven and muffin tin. Preheat the oven to 350 degrees Fahrenheit and then add 12 muffin liners to a standard muffin tin. Be sure to spray with a non-stick cooking spray to prevent the muffins from sticking to the liners.

    STEP 2: Combine dry ingredients. In a medium bowl, add the flour, ground flax seed, pumpkin pie spice, cinnamon, baking soda, and salt. Stir to combine. Then set aside.

    STEP 3: Whisk wet ingredients. In a large bowl, whisk together the eggs, pumpkin puree, greek yogurt, applesauce, oil, and vanilla.

    STEP 4: Combine wet and dry ingredients. Add the dry ingredients to the wet ingredients and gently fold together until well incorporated.

    STEP 5: Scoop batter. Scoop the muffin batter evenly into 12 muffin cups until they are around ⅞ of the way full. The liners will be quite full.

    STEP 6: Top with cinnamon sugar. In a small bowl, mix together the coconut sugar and cinnamon. Then sprinkle the mixture on top the unbaked muffins. Use all the cinnamon sugar for best flavor and results.

    STEP 6: Bake. Bake the muffins for 30-35 minutes or until a toothpick comes out clean. Let the muffins cool for 15 minutes in the pan before serving.

    As the pumpkin muffins bake, they will make your house smell AMAZING!

    NOTE: These muffins have a fluffy, spongy texture. They're light and airy, unlike a dense muffin, which keeps you from feeling sluggish after enjoying one (or two or three, like I did)!

    a stack of pumpkin muffins with a bite taken out

    Gluten-Free, Vegan Pumpkin Muffins

    If you need to make these pumpkin protein muffins gluten-free or vegan, you can make the following changes. I have not tested all of these suggestions, but expect they will work well.

    NOTE: Please don't try to make the muffins gluten-free AND vegan. I do not think they will turn out as they should when making that many changes.

    • Gluten-free pumpkin muffins - use a gluten-free flour blend in place of the pastry flour. Coconut sugar is naturally gluten-free, but be sure that the brand you use is manufactured in a gluten-free facility to be safe.
    • Vegan pumpkin muffins - instead of using chicken's eggs, use two flax eggs. Combine two tablespoons ground flax seed with six tablespoons water. Stir, then let stand for 10 minutes to thicken. If you use flax eggs, please know the muffins will have a lower protein content.

    I can't guarantee your results by making these changes, so please use caution when attempting to make the muffins differently then stated in the original recipe.

    Variations to the Muffins

    If you're hoping for a distinct taste, you can make a few variations to the pumpkin muffins to ensure they're exactly what you had in mind.

    • Spicy muffins - if you want that strong, fall spice flavor, use three tablespoons pumpkin pie spice and two tablespoons cinnamon, instead of one teaspoon.
    • Sweet muffins - these muffins are not very sweet by themselves. For a sweeter bite, use sweetened applesauce and add ½ cup coconut sugar to the batter.
    • Toppings - instead of a cinnamon sugar topping, you can use chocolate chips instead.
    a pumpkin muffin on a plate with a fork digging in

    Storing the Muffins

    You can keep the muffins covered on the counter for 24 hours, or keep in an airtight container in the fridge for 5-7 days. If you want to freeze the muffins, wrap them in clingwrap or store them in an airtight container.

    Be sure to warm the muffins after thawing from the freezer for the best flavor.

    More Recipes To Enjoy

    Blueberry Applesauce Muffins
    These blueberry applesauce muffins are made with whole wheat flour and are naturally sweetened, making them super healthy and low calorie. They only require 10 ingredients to make, and can easily be made vegan, too!
    Check Out This Recipe
    blueberry muffin on a plate
    Cinnamon Apple Waffles
    These apple cinnamon waffles are made with unsweetened applesauce and whole wheat flour which makes them super healthy. Each waffle packs 7g fiber, 6g protein, and only 3g of natural sugar. They have fresh apple chunks inside and plenty of fall spices that add so much flavor. Top them with coconut whipped cream, fresh apple slices, and maple syrup!
    Check Out This Recipe
    an apple cinnamon waffle with whipped cream and fresh apple slices
    Vegan Pumpkin Banana Bread
    This super moist vegan pumpkin banana bread is healthy and super easy to make at home. It is an eggless pumpkin bread with sweet hints of banana flavor and plenty of fall spices. Mix in chopped walnuts and vegan chocolate chips for a bite that you can't resist!
    Check Out This Recipe
    vegan pumpkin banana bread on a gray tray, with chopped walnuts baked on top the bread.

    If you make these muffins, I would greatly appreciate a comment or review below. Share a photo on Instagram and tag me, @savorthespoonful, so I can see your delicious bake!

    Recipe

    a stack of pumpkin protein muffins with a bite taken out

    Pumpkin Protein Muffins

    These pumpkin protein muffins have a delicious cinnamon sugar topping that make them absolutely delicious. Made with pure pumpkin, greek yogurt, and NO protein powder, these muffins are healthy and perfect for fall. This is a quick and easy recipe to make for Halloween, Thanksgiving, and your favorite fall events. They have such a fluffy texture that everyone is sure to enjoy.
    5 from 9 votes
    Print Recipe Pin Recipe
    Prep Time 15 mins
    Cook Time 30 mins
    Total Time 45 mins
    Course Breakfast, Dessert
    Cuisine American
    Servings 12 muffins
    Calories 124 kcal

    Ingredients
      

    Dry Ingredients

    • ¾ cup whole wheat pastry flour (or white whole wheat flour)
    • ⅔ cup ground flax seed
    • 3 tablespoons pumpkin pie spice
    • 1 teaspoon ground cinnamon
    • 1 teaspoon baking soda
    • ½ teaspoon salt

    Wet Ingredients

    • 2 eggs
    • ¾ cup 100% pure pumpkin puree (not pumpkin pie filling)
    • ¾ cup vanilla greek yogurt
    • ½ cup unsweetened applesauce
    • 1 tablespoon coconut oil melted
    • 1 teaspoon pure vanilla extract

    Cinnamon Sugar Topping

    • ¼ cup coconut sugar
    • 3 teaspoons ground cinnamon

    Instructions
     

    • Preheat the oven to 350 degrees Fahrenheit and add 12 silicone muffin liners to a standard muffin tin. If using paper liners, spray with a non-stick cooking spray to prevent the muffins from sticking to the liners.
    • In a medium bowl, add the flour, ground flax seed, pumpkin pie spice, cinnamon, baking soda, and salt. Stir to combine. Then set aside.
    • In a large bowl, whisk together the eggs, pumpkin puree, greek yogurt, applesauce, oil, and vanilla.
    • Add the dry ingredients to the wet ingredients and gently fold together until well incorporated.
    • Scoop the muffin batter evenly into 12 muffin cups until they are around ⅞ of the way full.
    • In a small bowl, mix together the coconut sugar and cinnamon. Then add the cinnamon sugar topping evenly on top the muffin batter. Use all the cinnamon sugar for best results.
    • Bake the muffins for 30-35 minutes or until a toothpick comes out clean. Let the muffins cool for 15 minutes in the pan before serving.
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    Reader Interactions

    Comments

    1. Andrea White says

      October 06, 2021 at 11:25 pm

      5 stars
      These muffins are the best! Nothing like a sweet and protein-packed breakfast to start the day with!

      Reply
    2. Emily Flint says

      October 07, 2021 at 12:45 am

      5 stars
      So moist and delicious! These pumpkin muffins didn't stand a chance in my house!

      Reply
    3. Giangi Townsend says

      October 07, 2021 at 1:12 am

      5 stars
      Delicious, moist, and so easy to make.
      Thank you for sharing

      Reply
    4. Linda says

      October 09, 2021 at 5:26 pm

      5 stars
      Coconut palm sugar is my favorite -- what I use in my coffee if I'm treating myself. I've never made cinnamon sugar with it, though...and can't wait to try it. I bet it has a little toasty note. Super excited to make this with one of the bazillion cans of pumpkin I just bought!

      Reply
    5. Kayla DiMaggio says

      October 09, 2021 at 7:07 pm

      5 stars
      Yum! These pumpkin protein muffins were so delicious! I loved all the flavors and they were so filling!

      Reply
    6. Dawn Conklin says

      October 10, 2021 at 1:27 am

      5 stars
      These pumpkin muffins are so delicious and easy to make! The whole family loved them and asked if I could make them again the next day!

      Reply
    7. Gabriela Herrera says

      October 11, 2021 at 1:17 am

      5 stars
      These muffins are perfect for meal prep and so packed with protein.

      Reply
    8. Mihaela | https://theworldisanoyster.com/ says

      October 11, 2021 at 8:41 am

      5 stars
      I love that you use coconut sugar as opposed to refined sugar:) I so wish I had a muffin ready for coffee right now!

      Reply
    9. Cindy Mom the Lunch Lady says

      October 11, 2021 at 7:01 pm

      5 stars
      These muffins sound wonderful. I love that you added chia seeds in them! These would be a great way to start the day.

      Reply
    10. Claire S says

      March 29, 2022 at 7:50 pm

      Can you make these gluten free? Sub with a gluten free baking flour?

      Reply
      • Samantha Ensinger says

        March 29, 2022 at 9:40 pm

        Hi Claire! Great question. I have not tested these muffins with other flours yet, so I can not guarantee how they will turn out with a substitute. However, I think you could give gluten-free all-purpose flour a try if it has xanthan gum in the ingredients list. Please let me know how they work out for you!

        Reply

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    Samantha, owner of savor the spoonful

    Hi, I'm Samantha! I created Savor The Spoonful during my sophomore year of college with the goal of sharing dietary-friendly recipes that are truly delicious. I'm passionate about inspiring others to live a life without food rules and dieting. That means enjoying desserts like these, and having fun while doing so. Learn more about me.

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