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    Home » Muffins

    Chocolate Pumpkin Protein Muffins (Gluten Free, Paleo)

    Published: Oct 28, 2025 · by Katie

    Jump to Recipe·Print Recipe

    These chocolate pumpkin protein muffins are soft and fluffy with a decadent chocolate flavor. They're made with canned pumpkin, almond butter and protein powder; making these protein muffins gluten free, dairy free and paleo.

    Chocolate pumpkin protein muffins on wire cooling rack.

    My kids will never turn down a chocolate muffin, so I made it my mission to create a muffin recipe with added protein and hidden veggies (aka pumpkin). And let me tell you, these chocolate pumpkin protein muffins have been a huge hit!

    These muffins are made with canned pumpkin puree (homemade would work just as well), almond butter and protein powder. They are completely flourless and paleo friendly, with a good dose of protein and extra nutrients from the pumpkin.

    These healthy protein muffins have a soft, fluffy texture with chunks of chocolate in every bite. My kids love them and I feel good knowing they're not eating a muffin disguised as cake (like most store bought muffins).

    Why You'll Love these Chocolate Pumpkin Protein Muffins

    • paleo - made with healthy, minimally processed ingredients you can feel good about
    • gluten free and dairy free - these muffins use a combination of almond butter, eggs, pumpkin, pea protein and cocoa powder. No milk, butter or flour.
    • flourless - made without flour
    • added protein - each muffin contains a little over 7 grams of protein
    • easy to make - a one-bowl batter that's baked in the oven for less than 30 minutes
    Holding a muffin with a bite out of it.

    Ingredients

    The full recipe for these chocolate pumpkin protein muffins can be found in the recipe card below, but here is an overview of the ingredients you will need:

    • almond butter - I recommend an almond butter that's made with only dry roasted almonds, nothing else
    • pumpkin puree - I like to use organic canned pumpkin puree.
    • maple syrup - to sweeten the muffins. You can swap the maple syrup for any other liquid sweetener.
    • large eggs - to bind the ingredients and give the muffins structure. Because this is a flourless recipe, I do not recommend an egg replacement.
    • vanilla extract - added for flavor
    • protein powder - I recommend using pea protein for this recipe. A plain, chocolate or vanilla pea protein would work well. Pea protein tends to be very absorbent, so other types of protein powder may not work well for this recipe.
    • cocoa powder - since these are chocolate protein muffins. I like using an organic Dutch processed cocoa powder.
    • baking powder - I either make my own paleo baking powder or use Otto's Naturals grain free baking powder.
    • baking soda - for the rise.
    • salt - enhances the flavors.
    • miniature dark chocolate chips - optional mix-in
    Ingredients needed to make flourless chocolate pumpkin protein muffins.

    How to Make Chocolate Pumpkin Protein Muffins

    This is a one-bowl muffin recipe - super easy! Here are the steps:

    1. First, preheat your oven to 350 degrees F. Line a muffin pan with 12 silicone or paper muffin liners.
    2. In a large mixing bowl, combine the wet muffin ingredients.
    3. Mix in the dry ingredients.
    4. Fold the chocolate chips into the batter.
    Step by step process for how to make chocolate pumpkin protein muffins.
    1. Scoop the batter into your lined muffin pan, filling each slot about ¾ full.
    2. Place the muffins in your oven and bake at 350 degrees F for 22-25 minutes. I think these muffins are best a little under-baked, giving the inside a more gooey texture.
    3. After baking, remove the muffins from the oven. Let them cool about 5 minutes in the muffin pan, then transfer them to a wire cooling rack.

    Tips and Tricks

    • Measure ingredients by weight. I always measure my flours by weight, as it's far more accurate than measuring by volume. You can use a small kitchen scale (super affordable off Amazon) to measure the ingredients that are given in grams.
    • Use organic canned pumpkin - organic pumpkin puree can have a different texture than conventional brands, which can change the muffin texture. So I recommend using organic for this recipe.
    • Use pea protein - this chocolate muffin recipe has only been tested with pea protein. While some other protein powders may work, I cannot guarantee results. Pea protein tends to be very absorbent, so using another type of protein powder may greatly change the texture of the muffins.
    • Mix up the add-ins. Feel free to leave out the chocolate chips and mix in some nuts, seeds or shredded coconut.
    Freshly baked muffins in muffin tin.

    Storage

    These muffins should be kept in an airtight container or baggie. They will last at room temperature for a couple days, up to 2 weeks in the fridge, or up to 2 months in the freezer.

    FAQ

    Can I swap the almond butter for another nut/seed butter?

    Yes, any nut or seed butter will work in place of the almond butter, with just a slight variation to the muffin texture.

    Can I use any type of protein powder?

    I have only tested these chocolate pumpkin protein muffins with pea protein, so that's the only type of protein powder I can recommend. Pea protein tends to be very absorbent, so keep that in mind if you try replacing it.

    More Gluten Free Protein Muffin Recipes

    Looking for other recipes like this? Try these:

    • Paleo pumpkin protein muffins on wire rack.
      Paleo Pumpkin Protein Muffins (No Yogurt, Gluten Free)
    • 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)
    • bite of protein muffin
      Low Carb Strawberry Protein Muffins
    Print
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    Chocolate pumpkin protein muffins on wire cooling rack.

    Chocolate Pumpkin Protein Muffins (Gluten Free, Paleo)

    5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 1 review
    • Author: Katie
    • Prep Time: 10 minutes
    • Cook Time: 22 minutes
    • Total Time: 32 minutes
    • Yield: 12 muffins 1x
    Print Recipe
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    Description

    These muffins have a sweet chocolate flavor and a fluffy, moist texture. They're gluten free, dairy free and paleo friendly.


    Ingredients

    Scale
    • ¾ cup organic pumpkin puree
    • 3 large eggs
    • ½ cup almond butter (just dry roasted almonds)
    • ⅓ cup maple syrup
    • 1 tsp vanilla extract
    • ½ cup pea protein (50g)
    • ¼ cup Dutch processed cocoa powder (24g)
    • 1 tsp paleo baking powder
    • ½ tsp baking soda
    • ½ tsp salt
    • ¼ cup miniature dark chocolate chips (optional)


    Instructions

    1. Preheat your oven to 350 degrees F.  Line a muffin pan with 12 silicone or paper muffin liners.
    2. In a large mixing bowl, combine the wet muffin ingredients.  This includes the pumpkin, eggs, almond butter, maple syrup and vanilla.
    3. Mix in the dry ingredients.  This includes the pea protein, cocoa powder, baking powder, baking soda and salt.
    4. Fold the chocolate chips into the batter.
    5. Scoop the batter into your lined muffin pan, filling each slot about ¾ full.
    6. Place the muffins in your oven and bake at 350 degrees F for 22-25 minutes.  I think these muffins are best a little under-baked, giving the inside a more gooey texture.
    7. After baking, remove the muffins from the oven.  Let them cool about 5 minutes in the muffin pan, then transfer them to a wire cooling rack.
    8. Store the muffins in an airtight container or baggie; up to 2 days at room temperature, 2 weeks in the fridge, or 2 months in the freezer.

    Notes

    Please note, nutrition facts are an estimate and calculated based on the exact brands I used.


    Nutrition

    • Serving Size: 1 muffin (out of 12)
    • Calories: 167
    • Fat: 10g
    • Carbohydrates: 13.4g
    • Protein: 7.5g

    Did you make this recipe?

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

    Pinterest image for chocolate pumpkin protein muffins.
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    Comments

    1. Katie

      November 02, 2025 at 5:55 pm

      My family and I love these protein muffins. Enjoy!

      Reply

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    I'm Katie and I have a passion for baking healthy treats using real, whole food ingredients. On my blog you'll find a variety of sweet and savory recipes, all gluten free and dairy free. My mission is to make baking nutritious, delicious, simple and family friendly.

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