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    Home » Paleo

    Paleo Pumpkin Protein Muffins (No Yogurt, Gluten Free)

    Published: Sep 5, 2025 · by Katie

    Jump to Recipe·Print Recipe

    These paleo pumpkin protein muffins are moist and tender with a lovely pumpkin flavor. They're made with cassava flour and pea protein and sweetened with coconut sugar.  In addition, this protein muffin recipe is paleo, gluten free, dairy free and made without yogurt.

    Paleo pumpkin protein muffins on wire rack.

    I've been making these pumpkin protein muffins for years because they're just the best way to ring in the fall months!

    They have a soft, tender texture - not dry or gummy like some protein muffins can be. Plus, these paleo pumpkin protein muffins take minimal effort and my kids love them. They're a great way to sneak extra protein in at breakfast or lunch.

    These protein muffins are made with cassava flour and pea protein and sweetened with coconut sugar (or monk fruit). Their flavor isn't overwhelming, which is probably why my kids like them. It's more of a mildly sweet pumpkin flavor. Sometimes we add in a few dark chocolate chips or top them with a simple glaze as a fun treat.

    Why You'll Love these Pumpkin Protein Muffins

    • paleo & gluten free - made with cassava flour and sweetened with coconut sugar.
    • dairy free - no yogurt or milk
    • nut free - perfect for anyone with nut allergies or intolerances
    • fluffy & moist - not dry or gummy like many protein muffin recipes
    • easy to make - a simple, one bowl muffin recipe that bakes in under 30 minutes!
    Holding a muffin with a bite out of it to show the inside texture.

    Ingredients

    Here's what you need to make these gluten free pumpkin protein muffins:

    • pumpkin puree - I like using organic canned pumpkin. It can be thicker than non-organic varieties, so please note that when making this recipe.
    • eggs - helps bind the ingredients. I have not tested an egg substitute, but if you do so then let me know how the muffins turn out in the comment section below.
    • vanilla extract - added for flavor
    • water - to thin the batter. You can swap the water with any other milk, like almond milk.
    • cassava flour - makes these muffins soft and fluffy, while keeping this recipe paleo friendly (and nut free). I have not tested any substitutes, but oat flour or a gluten free blend should work as a 1:1 swap if measured by weight (given in grams).
    • pea protein powder - pea protein is very absorbent, so other types of protein powders may not work for this recipe. I have used both unflavored pea protein and vanilla pea protein - both are great.
    • coconut sugar - to sweeten the muffins. You can swap coconut sugar for another granulated sugar like monk fruit.
    • pumpkin pie spice - adds more pumpkin flavor. This ingredient can be substituted with cinnamon or left out.
    • baking soda - for the rise.
    • salt - enhances the flavors.
    Ingredients needed to make paleo pumpkin protein muffins.

    How to Make Pumpkin Protein Muffins

    I'm all about the one bowl method when it comes to baking.  Meaning, place all your ingredients in one bowl, mix, pour into baking pan/muffin molds and bake! This easy pumpkin protein recipe is no different.

    1. First, preheat your oven to 350 degrees F. Line a muffin tin with 10 cupcake liners (paper or silicone work).
    Batter for muffins.
    1. Combine the wet muffin ingredients, then mix in the dry.
    Muffin batter in lined muffin pan.
    1. Scoop the batter into your lined muffin tin, filling each slot just over half way full.
    1. Place the muffins in your oven and bake in at 350 degrees F for 23-25 minutes.
    2. After baking, let the pumpkin muffins cool for a few minutes in the baking pan, then transfer them to a wire cooling rack.
    Top view of pumpkin protein muffins on wire cooling rack.

    Storage

    Like most paleo baked goods, I suggest storing these protein muffins in an airtight container in the fridge.  They will last a couple days at room temperature, but can be stored up to 10 days in the fridge.

    FAQ

    Do I have to use pea protein?

    Pea protein is very absorbent, so if you swap it with another protein powder you probably won't have the right batter texture, and in return a different texture in the baked muffins. You may be able to swap pea protein for another protein powder and decrease the water content. However, I have not tried any swaps, so can't give you exact measurements.

    Is there a swap for cassava flour?

    While I have only tested these pumpkin protein muffins with cassava flour, you should be able to use oat flour or a gluten free blend as a swap. For best results, I suggest measuring by weight (given in grams) instead of volume.

    More Healthy Protein Muffin Recipes

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    • Grabbing a banana protein muffin with a bite out of it to show the inside texture.
      Gluten Free Banana Protein Muffins (No Flour)
    • protein-muffins-recipe
      Vanilla Protein Muffins (Low Carb, No Banana)
    Print
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    Paleo pumpkin protein muffins on wire rack.

    Paleo Pumpkin Protein Muffins (No Yogurt, Gluten Free)

    5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 1 review
    • Author: Katie
    • Prep Time: 5 minutes
    • Cook Time: 24 minutes
    • Total Time: 29 minutes
    • Yield: 10 muffins 1x
    Print Recipe
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    Description

    Moist and tender paleo pumpkin protein muffins made with pea protein and cassava flour.  Healthy enough for breakfast or an afternoon snack.


    Ingredients

    Scale
    • ½ cup pumpkin puree
    • 3 large eggs
    • ½ cup water (or almond milk)
    • 1 tsp vanilla extract
    • ½ cup cassava flour (70g)
    • ½ cup pea protein powder (55g)
    • ¼ cup coconut sugar (or monk fruit sweetener)
    • 1 tsp pumpkin pie spice
    • ½ tsp baking soda
    • ¼ tsp salt


    Instructions

    1. Preheat your oven to 350 degrees F. 
    2. Line a muffin pan with 10 cupcake liners (paper or silicone) and set aside.
    3. In a medium-sized mixing bowl, whisk together the wet ingredients.  This includes the eggs, pumpkin, vanilla and water.
    4. Add in dry ingredients (cassava flour, pea protein, sweetener, pumpkin spice, baking soda and salt) and whisk until smooth.
    5. Pour about ¼ cup batter into each muffin slot, filling them just over half way.
    6. Place the muffins in the oven and bake at 350 degrees for 23-25 minutes.
    7. After baking, remove the muffins from the oven and let them rest a few minutes in the baking pan.  Then transfer them to a wire cooling rack.
    8. Best stored in an airtight container in the fridge, up to 10 days.

    Did you make this recipe?

    Share a photo and tag me — I can't wait to see what you've made!

    Pinterest image for gluten free pumpkin protein muffins.
    « Olive Oil Pumpkin Bread (Gluten Free, Paleo)
    Gluten Free Pumpkin Cake (Egg Free, Nut Free) »

    Reader Interactions

    Comments

    1. WholisticallyHannah

      October 02, 2017 at 12:53 pm

      YUM! These sound fantastic. I've never heard of cassava flour before - I'll have to look into it!

      Reply
      • realfoodrabbit

        October 03, 2017 at 1:49 pm

        Thank you! You must give cassava flour a try - it's one of my favorite gf baking flours 🙂

        Reply
      • MrsC5

        September 20, 2024 at 5:10 am

        I'd love to try these, but curious about substituting another protein powder for the Pea powder. I have to avoid legumes. Thanks in advance

        Reply
        • Katie

          September 20, 2024 at 7:03 am

          What protein powder were you looking to try? Pea protein is very absorbent, so keep that in mind if you're trying another protein powder.

    2. paulettemotzko

      October 25, 2017 at 9:35 pm

      Your muffins look great.

      Polly Motzko

      Reply
      • realfoodrabbit

        October 26, 2017 at 2:16 pm

        Thank you! 🙂

        Reply
      • Valerie

        September 22, 2021 at 4:12 pm

        Can the protein powder be omitted or do you have to replace it with something else?

        Reply
        • Katie

          September 23, 2021 at 5:54 am

          The protein powder is necessary for this recipe.

    3. Michelle

      September 11, 2018 at 8:57 pm

      I tried these with pea protein and I’m sorry to say they were horrible! ????

      Reply
      • realfoodrabbit

        September 13, 2018 at 5:48 am

        I'm so sorry to hear that! What didn't work? Taste? Texture? Did you use sweetened pea protein?

        Reply
    4. Katie

      November 30, 2021 at 6:13 am

      These are some of my favorite protein muffins. Hope you all love them!

      Reply
    5. Kwoods

      December 24, 2021 at 7:57 am

      Do you have nutritional info?

      Reply
    6. Chris

      May 03, 2024 at 8:42 am

      Can this be made in a bread pan vs muffin cups?

      Reply
      • Katie

        May 03, 2024 at 12:11 pm

        That should work! The bake time will probably increase.

        Reply
        • Jamey G Erb

          October 13, 2024 at 8:47 pm

          Do these have to be refrigerated?

        • Katie

          October 14, 2024 at 6:28 am

          No, you can store them at room temperature for a couple days.

        • Jean Allen

          September 07, 2025 at 8:40 am

          Hi, Katie! I was wondering about making these as a bread, too! 🙂 Besides an increase in baking time (like most pumpkin breads), do you have an estimate as to quantity for either 1 or 2 loaves? I used to like making 2 loaves at a time with my old wheat flour recipe because I could gift or freeze the second one. 😋

        • Katie

          September 07, 2025 at 7:40 pm

          Hi! I imagine these muffins would only equate to one small loaf. I would at least double it to make two.

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