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    Home » Recipes » Healthy Dairy and Gluten-Free Snack Recipes

    Pumpkin Protein Muffins [Gluten-Free]

    Modified: Sep 4, 2025 · by Shelby Stover · This post may contain affiliate links · 12 Comments

    Jump to Recipe
    Close up of a pumpkin protein muffin with chocolate chips with a bite out of it and text above the image.

    Love fall flavors but hate the classic crash? These Pumpkin Protein Muffins are soft, packed with pumpkin spice, and loaded with gooey chocolate chips, making them the perfect way to satisfy your sweet tooth and keep your energy up. Baked in just 25 minutes, they're a mouthwatering way to cozy up with a fueling snack.

    Pumpkin protein muffins on a black cooling rack with one muffin in front of it and chocolate chips around it.

    “These were the perfect afternoon pick me up - not too much hassle to make and tasted DELICIOUS!! Thank you!!!”

    - Ali

    A Quick Look At The Recipe

    • ⏲️Ready In: 45-50 Minutes
    • 👪Serves: 12
    • 🍽 Calories and Protein: 116 kcals and 8 grams of protein
    • 📋 Main Ingredients: 1:! Gluten-free baking flour, protein powder, pumpkin puree, and maple syrup.
    • 📖 Dietary Notes: Dairy-free and gluten-free
    • ⭐ Why You'll Love It: Packed with fall flavor, these pumpkin protein muffins taste like dessert but fuel like breakfast.

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    These pumpkin protein muffins are everything you want in a fall snack: soft, spiced, chocolatey, and secretly packed with protein just like this pumpkin protein mug cake. Made with protein powder and a few gluten-free food staples, they’re a cozy, feel-good treat you’ll want on repeat (just like this pumpkin protein overnight oats recipe!).

    Even my kids devour them straight from the oven, which is a win in my book. As a mom and coach, it’s rare to find a recipe that fuels your body and makes your whole house smell like pumpkin pie. Learn more about the benefits of a high protein diet and why you want to amp it up!

    Jump To
    • A Quick Look At The Recipe
    • 💭Why You'll Love This Recipe
    • Ingredients You’ll Need
    • Flavor Variations
    • Expert Tips
    • How To Make Pumpkin Protein Muffins
    • Choosing A Protein Powder
    • Pumpkin Protein Muffins FAQs
    • High Protein Pumpkin Recipes
    • High Protein Pumpkin Muffins (Gluten-Free)

    💭Why You'll Love This Recipe

    Easy to make: Made with high-protein food staples, all you have to do is mix everything in a bowl and bake!

    Fueling: These protein pumpkin muffins come with 8 grams of protein in each muffin. Grab two muffins for a snack and you're all set.

    Allergy-friendly: The muffins are naturally dairy-free and gluten-free.

    On-the-go snack: You won’t get stuck on busy days if you have these on hand!

    Ingredients You’ll Need

    Ingredients to make pumpkin protein muffins in measuring cups with text labels over top.

    1:1 Gluten-free baking flour: Gluten-free flours tend to absorb liquid, so don’t overlook letting the batter set a bit.

    Protein powder: This protein pumpkin muffins recipe has been made with multiple protein powders. See the adjustments in the recipe card to adapt the recipe as needed. Know that the kind of protein you choose affects the texture and taste.

    Pumpkin pie spice: Feel free to add a smidge more if you’re a die-hard (these gluten-free pumpkin donuts are a great way to get your fix on too!).

    Canned pumpkin: Don’t confuse this with pumpkin pie filling, which will be too sweet.

    Dairy-free milk: We use homemade hemp milk the most,t but any non-dairy milk will work.

    See the recipe card for full information on ingredients and quantities

    Flavor Variations

    • Chocolate pumpkin: Use a chocolate protein powder to give the gluten-free pumpkin muffins a bold chocolate flavor.
    • Pumpkin spice latte: Add a dash of espresso powder to the muffins to create a total PSL taste.
    • Dessert-like: Muffins can always be dressed up to become more indulgent. Drizzle these high-protein pumpkin muffins with dairy-free cream cheese frosting or homemade caramel with coconut milk to make them extra indulgent, like these caramel apple overnight oats.

    Looking for more high-protein ways to satisfy your craving? Check out the Strong and Sweet Protein Guide that has easy snacks that taste like dessert with 17 grams of protein or more.

    Expert Tips

    Don’t overlook letting the batter sit for a minute or two. Gluten-free flours take a minute to absorb, and this way your high-protein pumpkin muffins all come out evenly.

    Use a silicone muffin tin or silicone muffin liners. This makes it much easier to remove the muffins.

    You can use mini chocolate chips or regular, but the regular ones make it so that you’ll have big, gooey bites (so worth it!).

    Let the muffins cool once cooked as this allows them to firm up. If you remove them from the mold before they're cooled, you risk breaking them.

    The kind of protein powder you choose will change the entire structure of the pumpkin muffins.

    How to store them: I keep the pumpkin protein muffins in an airtight container on the counter for 1-2 days. Or, keep them in the fridge for 3-5 days.

    How To Make Pumpkin Protein Muffins

    Glass bowl with flour, chocolate chips, and protein powder in it with measuring cups around it with maple syrup and pumpkin puree.

    Step 1: In a large bowl combine all the dry ingredients and mix well.

    Glass bowl with pumpkin puree, flour, and protein powder with measuring bowls around it and a spoon in the bowl.

    Step 2: One by one add in the eggs, maple syrup, pumpkin, vanilla, and dairy-free milk.

    Glass bowl with raw pumpkin protein batter and a black spoon in it with measuring cups around it.

    Step 3: Stir to combine and let sit for 2-3 minutes. Then, restir the batter.

    Steel muffin in with raw pumpkin protein muffin batter.

    Step 4: Portion the batter into a lined muffin tin and bake for 25 minutes keeping a close eye on the muffins in the last few minutes.

    Choosing A Protein Powder

    The texture and taste will chnage based on the protein powder you choose. Originally, these pumpkin protein muffins were made with Naked Nutrition's Rice Protein Powder and if you're using a rice protein powder, follow the recipe as writen.

    To make the muffins with pea protein powder: Follow the recipe as-written but only use 1 tablespoon of dairy-free milk.

    For fermented protein powder: Use the following measurement swaps. ¾ cups of protein powder, ¾ teaspoons of baking powder, and a full ¾ cups of dairy-free milk. Bake them for 20-25 minutes and know that the recipe makes about 8 muffins. 

    Using beef protein powder: This is all I use currently (read the benefits of beed protein powder), and I made the recipe with Paleo Pro protein (code mamabear saves you money) To do this, use ⅓ cup + 2 tablespoons of protein powder, cut the maple syrup to ⅓ cup and eliminate the non dairy milk. This makes 11 protein muffins. So far, this has been my favorite texture of the muffins.

    Pumpkin Protein Muffins FAQs

    Is pumpkin considered a superfood?

    Pumpkin is loaded with vitamins and fiber making it an awesome addition to your diet. Given this, all foods can technically be superfoods. However, pumpkin is high in some of the nutrients we don’t get enough of (like zinc) making it a step above other foods.

    Do pumpkin muffins taste “healthy”?

    Pumpkin muffins taste like any other muffins and much of it comes down to the other ingredients used. Because these protein pumpkin muffins are sweetened with only maple syrup and chocolate chips, they will have a healthier taste to them than a traditional, store-bought muffin.

    When is the best time to eat protein muffins?

    Protein muffins make wonderful snacks throughout the day. They’re not crazy high in protein which makes them a good snack between your bigger meals.

    How do I make mini pumpkin protein muffins?

    To make mini pumpkin protein muffins simply use a mini muffin tin with paper liners and only bake the protein muffins for 18-20 minutes watching them closely in the last few minutes so that they don't burn.

    Close up of a pumpkin protein muffin with chocolate chips with a bite out of it.

    High Protein Pumpkin Recipes

    • Multiple pumpkin protein balls on a white plate and more on a fall decoration behind it.
      Pumpkin Spice Protein Balls [No Bake]
    • Pumpkin protein pudding in a jar topped with cinnamon and a spoon in the jar.
      High Protein Pumpkin Pudding
    • Protein pumpkin bread sliced and topped with almonds on a cutting board.
      Protein Pumpkin Bread [Gluten-Free]
    • Mason jar with pumpkin spice overnight oats with cream cheese frosting on top and an orange linen and decorative pumpkins behind it.
      Pumpkin Protein Overnight Oats (Dairy-Free)

    If you tried this Protein Pumpkin Muffins Recipe or any other recipe on my blog, please leave a 🌟 star rating and let me know how it goes!

    High Protein Pumpkin Muffins (Gluten-Free)

    Shelby Stover
    Indulge in your favorite fall flavors with these pumpkin protein muffins! Made with vegan protein powder and sweetened with maple syrup these gluten-free muffins make the perfect on-the-go snack.
    5 from 5 votes
    Print Recipe Pin Recipe
    Prep Time 5 minutes mins
    Cook Time 25 minutes mins
    Cooling time 30 minutes mins
    Total Time 1 hour hr
    Course post-workout, Snack
    Cuisine American
    Servings 11
    Calories 116 kcal

    Video

    Equipment

    • Measuring Cups and Spoons
    • Trigger ice cream scoop
    • Silicone Muffin Molds

    Ingredients
      

    • ⅓ cup 1:1 Gluten-Free baking flour
    • 1 cup Vegan vanilla protein powder
    • 1 teaspoon Pumpkin pie spice
    • 1 teaspoon Baking powder
    • 1 teaspoon Cinnamon
    • 2 Eggs
    • 2 tablespoons Dairy-free milk
    • ½ cup Maple syrup
    • 1 teaspoon Vanilla extract
    • ½ cup Canned pumpkin
    • ¼ cup chocolate chips

    Instructions
     

    • In a large bowl combine all the dry ingredients and mix well.
    • One by one add in the eggs, maple syrup, vanilla, pumpkin, and dairy-free milk.
    • Stir to combine and let sit for 2-3 minutes.
    • Restir before portioning the batter into a silicone muffin tin.
    • Bake at 350 degrees Fahrenheit for 25 minutes.
    • Remove from the oven and let them cool fully before popping them out of the molds.

    Notes

    Nutrition is based on 8 muffins however, depending on your muffin tin it makes 8-11.
    Use silicone muffin molds so that the muffins slide out easily.
    Pumpkin puree, not pumpkin pie filling.
    Don’t overlook letting the batter sit for a minute or two. Gluten-free flours take a minute to absorb and this way your pumpkin protein muffins all come out evenly.
    You can use mini chocolate chips or regular, but the regular ones make it so that you’ll have big, gooey bites (so worth it!).
    Pear protein powder: Follow the recipe as-written but only use 1 tablespoon of dairy-free milk.
    Fermented protein powder: Use the following measurement swaps. ¾ cups of protein powder, ¾ teaspoons of baking powder, and a full ¾ cups of dairy-free milk. Bake them for 20-25 minutes and know that the recipe makes about 8 muffins. 
    Beef protein powder: This is all I use currently, and I made the recipe with Paleo Pro protein(code mamabear saves you money). To do this, use ⅓ cup + 2 tablespoons of protein powder, cut the maple syrup to ⅓ cup, and eliminate the non dairy milk. So far, this has been my favorite texture of the muffins.
    Storing them: I keep the pumpkin protein muffins in an airtight container on the counter for 1-2 days. Or, keep them in the fridge for 3-5 days. They tastes best after sitting for an hour or more. After being in the fridge they tend to firm up to perfection.
    Disclaimer:

    Nutrition values are estimates only, using online calculators. Please verify using your own data"

    Nutrition

    Calories: 116kcalCarbohydrates: 16gProtein: 8gFat: 2gSaturated Fat: 1gPolyunsaturated Fat: 0.2gMonounsaturated Fat: 0.3gTrans Fat: 0.01gCholesterol: 28mgSodium: 106mgPotassium: 101mgFiber: 1gSugar: 11gVitamin A: 1647IUVitamin C: 1mgCalcium: 54mgIron: 2mg
    Have You Tried This Recipe?Please leave a star rating and comment below. Mention @fitasamamabear or tag #fitasamamabear!
    Pumpkin protein muffins on a black cooling rack with one muffin a bite out of it and chocolate chips around it.

    More Healthy Dairy and Gluten-Free Snack Recipes

    • Peanut butter chocolate buckeyes on top of a parchment paper.
      Protein Buckeyes [Dairy-Free]
    • Squares of coffee fudge on a cutting board.
      Protein Coffee Fudge [Dairy-Free]
    • A stack of frozen yogurt bars.
      Frozen Yogurt Protein Bars [5 ingredients]
    • A bowl of baked banana bread with chocolate chips and sliced bananas on top.
      Single Serve Banana Bread (High Protein)

    Comments

    1. kim brown says

      October 25, 2023 at 4:26 pm

      I just tripled this recipe and they are currently in the oven. I didn't see until after the fact that your notes say not to use whey protein powder. what is going to happen?

      Reply
      • fitasamamabear says

        October 26, 2023 at 11:07 am

        So whey doesn't absorb like vegan protein powder does so the muffins most likely won't fluff up (vegan protein in some ways mimics flour). Let me know the result so that I can let others know more detail!

        Reply
    2. Jessica says

      August 30, 2023 at 4:25 pm

      5 stars
      I made a big batch of tallow and this was my first time ever using it for a baking recipe. They were moist, perfectly spiced, and so filling - a perfect breakfast or snack. They disappeared faster than I could blink!

      Reply
      • fitasamamabear says

        September 05, 2023 at 6:53 am

        Ah this makes my heart happy! Such a wicked healthy fat!

        Reply
    3. Julianne says

      August 30, 2023 at 12:08 pm

      5 stars
      These turned out great! I really love the use of maple syrup with the pumpkin and the chocolate chips were a nice bonus!

      Reply
      • fitasamamabear says

        August 30, 2023 at 1:20 pm

        Maple syrup is such a staple in our house! Works in everything.

        Reply
    4. Gina says

      August 30, 2023 at 10:53 am

      5 stars
      Your recipes are always the best! Love how I can enjoy this pumpkin muffin while still getting in some protein and nutrition, not just a carb bomb! These baked up with a great texture and flavor.

      Reply
      • fitasamamabear says

        August 30, 2023 at 1:20 pm

        Thank you for such a wicked compliment!!

        Reply
    5. Ali says

      August 30, 2023 at 10:02 am

      5 stars
      These were the perfect afternoon pick me up - not too much hassle to make and tasted DELICIOUS!! Thank you!!!

      Reply
      • fitasamamabear says

        August 30, 2023 at 1:20 pm

        Easy to make is definitely key in my house!

        Reply
    6. Shay L. says

      August 30, 2023 at 7:56 am

      5 stars
      I'm so glad it's pumpkin season again! I loved the maple syrup in these muffins, so good with pumpkin and pumpkin spice!

      Reply
      • fitasamamabear says

        August 30, 2023 at 1:20 pm

        Haha pumpkin season always comes in with a bang!

        Reply
    5 from 5 votes

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    Welcome!

    I'm Shelby, a Certified Strength & Nutrition Coach who has spent the last 10 years helping women feel more comfortable in their skin though home strength training and healthy food- no diets, no shortcuts

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