Pumpkin Protein Muffins

These warm, sweet, and tender pumpkin protein muffins disappear fast when we make them at home. As moms and registered dietitians, nothing makes us happier than having one of our real-food recipes win over every member of the family. These nutritious protein muffins do that, and they are so easy to make. In fact you can mix up the batter and have them in the oven in less than 10 minutes! They bake up tender and delicious with just the right amount of pumpkin flavor and crunchy pumpkin seeds to top it off.

If you love the pumpkin bread from Starbucks, consider this a Starbucks pumpkin bread clone recipe, just in muffin form (and with a lot less added sugar). Plus, we’ve made them high in protein and sans the gluten so you can feel good when this batch disappears fast in your home, too.

This post was created in partnership with The Strong Inside

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high-protein breakfast muffins for a healthy start

While many common breakfast foods tend to focus on carbohydrates (think hot and cold cereal, bars, baked goods, bagels and other breads), we always recommend starting the day with some protein. Why? Because there’s a lot of research that shows getting protein early in the day is beneficial for muscle growth (1), weight loss by increasing muscle mass (2), burning more calories (3), regulating blood sugar (4), and decreasing the desire to snack throughout the day (5).

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The whey protein powder, a protein from milk, gives these muffins a nutritious boost. Proteins from milk are considered a complete protein because they contain all the essential amino acids your body needs to thrive. And, unlike other protein powders that can be heavily processed and made from a long list of ingredients, whey protein is made simply from milk through filtration and pressure. Plus, whey protein powder releases quickly so your body can enjoy the benefits of proteins from milk right away.  

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Ingredients to make pumpkin protein muffins

Here’s what you need to make protein pumpkin muffins for a delicious and nutritious breakfast or snack that everyone will love:

  • Whey protein powder this tasteless powder adds clean, high-quality protein to each muffin without creating a chalky texture; use unflavored or vanilla
  • Gluten-free baking flour – we like Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour or King Arthur Measure-for-Measure Gluten-Free Flour. You can also use the same amount of regular all-purpose flour if you don’t need the muffins to be gluten-free
  • Canned pumpkin you’ll need one 15-ounce can of pure pumpkin puree (not pumpkin pie filling, which has added sugar)
  • Brown sugar can sub coconut sugar
  • Eggs for egg-free, you can make flax eggs. To replace the 2 eggs in this recipe, mix 2 tablespoons ground flaxseed meal with 1/3 cup of water and set aside for 15 minutes to thicken
  • Olive oil a necessary ingredient to create the right amount of moisture and tender texture in these muffins; can sub avocado oil
  • Maple syrup – use Grade A pure maple syrup for the best flavor
  • Vanilla extract
  • Pumpkin pie spice if you don’t have pumpkin pie spice, mix 1 teaspoon ground cinnamon, 1/2 teaspoon ground ginger, 1/4 teaspoon ground nutmeg, 1/4 teaspoon ground allspice, and a pinch of ground cloves
  • Baking soda
  • Salt we used fine sea salt, but you can use whatever salt you have on hand
  • Raw pumpkin seeds – we love pepitas (raw pumpkin seeds) for topping these muffins; if you want to get adventurous, read below for more muffin mix-ins and toppers you can use

How to make pumpkin protein muffins

This batter mixes up to a beautiful rustic fall pumpkin color. Here’s how easy it is to make this protein muffin recipe:

  1. In a bowl, combine the dry ingredients: the flour, whey protein powder, pumpkin pie spice, baking soda, and salt.
  2. In a separate bowl, combine the wet ingredients: the pumpkin puree, brown sugar, eggs, oil, maple syrup, and vanilla; mix well. Pour the wet ingredients into the dry ingredients and mix until well incorporated. 
  3. Divide the batter among 12 cups in a standard size muffin tin, placing about ¼ cup batter into each muffin cup. Smooth the batter slightly in each muffin cup with the back of a spoon or with a rubber spatula. Sprinkle chopped pumpkin seeds over the batter.  
  4. Bake and then enjoy one warm out of the oven!  

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Why we Choose whey, a protein from milk

Increasing the protein in any muffin recipe is a simple way to transform a regular baked good from carb-heavy, sugar-laden treat to functional food (that tastes good, too). Whey protein powder is a natural protein from milk and a real-food addition that can easily increase the protein in many recipes, helping you build muscle, recover after workouts, feel full longer, and be supported for higher protein needs for different life stages. We like using whey protein powder because it performs just as well in baked goods as it does in smoothies and adds healthy protein without leaving a chalky taste or texture. And, unlike other protein powders, whey protein powder is a natural ingredient that is simply made from milk.

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More Healthy High-Protein Recipes

We know proteins from milk have proven benefits, documented by a lot of science. Which is why we partnered with The Strong Inside to share how proteins from milk can help with your goals. Whether you’re looking to build strength, lose weight, or age healthfully, there is a protein from milk option for you. For more recipes that use proteins from milk (including breakfast, snacks, smoothies, and more) check out The Strong Inside.

Take Me To The Protein Recipes

toppers & Mix-ins for pumpkin protein muffins

This protein muffin recipe provides a wonderful backdrop for you to get creative with your mix-ins and toppers. You can easily stir 1/2 cup of one of these mix-in ingredients or sprinkle a handful on top of the batter without making any other changes to the recipe. Here are some ingredients that taste especially good in (and on top of) these pumpkin protein muffins:

  • pepitas (raw pumpkin seeds)
  • sunflower seeds
  • dried cranberries or cherries
  • chocolate chips
  • white chocolate pieces
  • chopped walnuts, pistachios, or hazelnuts
  • cooked and crumbled bacon
  • cinnamon-sugar (after baking, brush melted butter on the muffin tops and sprinkle with cinnamon-sugar)
  • cream cheese frosting (turn these protein muffins into protein cupcakes by adding a little homemade frosting on top; see the tip below)

Turn These Muffins Into Protein Cupcakes

Top these pumpkin protein muffins with cream cheese frosting to take them in a sweeter direction. Use the Cream Cheese Frosting recipe from our Soft Pumpkin Cookies with Cream Cheese Frosting recipe, which is quickly made from butter, cream cheese, vanilla, pumpkin pie spice, and powdered sugar.

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How to store & Freeze pumpkin protein muffins

Though these muffins tend to disappear within a day or two of being baked, they do store and freeze well. Store the completely cooled muffins in a covered container at room temperature for up to one week. Or, freeze the cooled muffins in a freezer-safe container for up to three months.

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Baking tips for pumpkin protein muffins

We learned a few key baking tips when perfecting this protein muffin recipe for you that will ensure perfectly baked pumpkin muffins every time.

  1. Mix well, but don’t over-mix. You don’t want to mix the batter so much that it becomes very dense and hard to stir. And on the other hand, you don’t want to mix the dry ingredients and the wet ingredients so little that all of the ingredients don’t properly intermingle.
  2. Mist the muffin tins with a light coating of nonstick spray. Since the batter is moist and contains oil, you likely won’t have much trouble with the muffins sticking to the pan. But consider nonstick spray a little extra insurance against sticking, no matter what type of muffin tin you use.
  3. Use whey protein powder as the protein-enhancing ingredient in this protein muffin recipe. It bakes well, is flavorless (though vanilla protein powder adds a nice subtle flavor), and doesn’t leave a chalky aftertaste or texture. The addition of 1/2 cup of whey protein powder adds 5 grams of high-quality protein to each muffin.
  4. Allow the muffins to cool while still in the muffin tin for just a few minutes. This helps create steam that releases the muffins from each cup. But, don’t leave the muffins in their cups for longer than 5 minutes after removing from the oven. The steam can make the muffins too soggy, so remove them from the muffin tin and let the individual muffins cool completely on a wire rack.

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A muffin recipe for all Occasions

Though they are essential for fall, pumpkin muffins are a crowd favorite any time of the year. Just ask the folks at Starbucks, who enthusiastically sell their famous pumpkin bread year round. And since this is the muffin format of a Starbucks pumpkin bread clone recipe, you can bet that these protein muffins will be a hit at occasions a-plenty. Serve these pumpkin muffins at birthday parties and showers, as an after-school snack, for weekend breakfasts and brunches, to take to a new mom or sick friend, or to the office snack station any time of year.

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Gluten-Free Pumpkin Protein Muffins

A delicious, moist pumpkin protein muffin recipe without the gluten and with added nutrition from whey protein powder. Makes for a nutritious addition to breakfast or a healthy family-friendly snack. The flavor and texture are so good, these muffins taste just like Starbucks’ pumpkin bread, just in muffin form and with a lot less sugar.

Prep: 10 minsCook: 18 to 20 minsTotal: 30 mins

Servings: 12 muffins 1x


  • 1¼ cups gluten-free baking flour blend (180 g)*
  • ½ cup whey protein powder (vanilla or unflavored) (40 g)
  • 2 teaspoons pumpkin pie spice**
  • 1 teaspoon baking soda
  • ½ teaspoon fine salt
  • 1 (15-oz) can pumpkin puree (not pumpkin pie filling)
  • ½ cup brown sugar (may sub coconut sugar) (100 g)
  • 2 whole eggs
  • ¼ cup olive oil or avocado oil
  • ¼ cup pure maple syrup (75 g)
  • 1 teaspoon pure vanilla extract
  • Raw green pepitas (pumpkin seeds), coarsely chopped (optional)


  1. Preheat the oven to 375 degrees. Mist the cups of a standard 12-cup muffin tin with cooking spray. 
  2. In a large bowl, combine flour, protein powder, pumpkin pie spice, baking soda, and salt. Toss to combine. 
  3. In another bowl, combine the pumpkin puree, brown sugar, eggs, oil, maple syrup, and vanilla; mix well. Pour the wet ingredients into the dry ingredients and mix until well incorporated. 
  4. Divide the batter among the 12 cups in the muffin tin (about ¼ cup batter into each muffin cup). Smooth the batter slightly in each muffin cup with the back of a spoon or with a rubber spatula. Sprinkle chopped pepitas over the batter.  
  5. Bake for 18 to 20 minutes. Remove from the oven and let cool a few minutes in the muffin tin before transferring to a wire rack to cool completely. 

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Store the cooled muffins in a covered container at room temperature for up to 1 week, or freeze in a freezer-safe container for up to 3 months.

*You can use the same amount (180 g) of unbleached all-purpose flour if you don’t need your muffins to be gluten free. For gluten-free baking flours, we like Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour or King Arthur Measure-for-Measure Gluten-Free Flour.

**If you don’t have pumpkin pie spice, you can make your own. To do so, mix 1 teaspoon ground cinnamon, 1/2 teaspoon ground ginger, 1/4 teaspoon ground nutmeg, 1/4 teaspoon ground allspice, and a pinch of ground cloves.

Nutrition Information

  • Serving Size: 1 muffin
  • Calories: 176
  • Fat: 5 g
  • (Sat Fat: 1 g)
  • Sodium: 226 mg
  • Carbohydrate: 25 g
  • (Fiber: 2 g
  • Sugar: 13 g)
  • Protein: 7 g
  • Cholesterol: 24 mg


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