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    You are at:Home»Dairy-Free Recipes»Bread»Chocolate Protein Muffins with Healthy Ingredient Options for All

    Chocolate Protein Muffins with Healthy Ingredient Options for All

    8
    By Alisa Fleming on July 29, 2023 Bread, Breakfast, Dairy-Free Recipes, Dairy-Free Snack Recipes
    Jump to Recipe Print Recipe

    Breakfast on the go? Check! Healthy natural ingredients? Check! Tasty indulgent flavor? Yes, these dairy-free chocolate protein muffins check all the boxes. They’re even relatively low in calories and sugars, and the recipe includes options for various allergies and dietary needs.

    Dairy-Free Chocolate Protein Muffins Recipe. Also naturally gluten-free, soy-free, and nut-free, with options for egg-free and vegan needs.

    Dairy-Free Chocolate Protein Muffins for the Whole Family

    This recipe for dairy-free chocolate protein muffins is a sample from The Gluten-Free Family Cookbook: Allergy-Friendly Recipes for Everyone Around Your Table by Lindsay Cotter of Cotter Crunch. I have answers to some common questions for both the recipe and her cookbook below.

    Where Can I Get Oat Flour? Can I Make My Own?

    I usually make it! Simply process oats in your blender, food processor, or spice grinder until a fine powder is achieved. This usually takes just a minute or two. To make 1 3/4 cups oat flour, you will need about 1 3/4 cups oats, or about 7 ounces / 195 grams. You can also buy oat flour. If you need strictly gluten-free, be sure to use oats or oat flour that are specifically tested for gluten-free diets.

    What Protein Powder Should I Use in these Chocolate Protein Muffins?

    For plant-based protein powder, Lindsay typically recommends Vega, Orgain, Garden of Life, or Huel. These do all contain pea protein. You can source a different type if you need legume-free.

    Can I Use a Different Flavor of Protein Powder?

    You can, but keep in mind that the protein powder provides most of the chocolate flavor. If you don’t want a chocolate-flavored protein muffin, omit the cocoa powder and use the higher amount of plain or vanilla protein powder.

    Where Can I Get Dairy-Free Dark Chocolate Chips?

    I like to use Enjoy Life Dark Chocolate Chips. They’re made free of top allergens, including milk. It’s Lindsay’s preferred brand too!

    Is The Gluten-Free Family Cookbook Dairy Free?

    Basically, it is. Lindsay provides option for various dietary needs. This does mean that dairy is an option in a few recipes, but all seem to be dairy free or have a dairy-free option.

    What Other Allergens Does this Cookbook Address?

    As you can guess by the title, it’s a strictly gluten-free cookbook. But unlike many other gluten-free cookbooks, Lindsay shuns gums and flour blends, and uses starch sparingly. She mostly utilizes oat, coconut, and occasionally almond for the flour. That said, most recipes are tree nut-free or have a tree nut-free option. She does use coconut a bit, but coconut is not a tree nut. The recipes are also soy-free and optionally egg-free.

    What Else Can You Tell Me About The Gluten-Free Family Cookbook?

    It’s a full color cookbook with over 75 allergy-friendly recipes. The focus is on healthy, easy food for both kids and adults. You’ll also find many fun everyday recipes, and options for vegetarian and vegan needs throughout!

    Dairy-Free Chocolate Protein Muffins Recipe. Also naturally gluten-free, soy-free, and nut-free, with options for egg-free and vegan needs.

    Special Diet Notes: Chocolate Protein Muffins

    By ingredients, this recipe is dairy-free / non-dairy, optionally egg-free, gluten-free, nut-free, peanut-free, soy-free, optionally vegan, plant-based, and vegetarian.

    Dairy-Free Chocolate Protein Muffins Recipe. Also naturally gluten-free, soy-free, and nut-free, with options for egg-free and vegan needs.
    Lindsay Cotter

    Dairy-Free Chocolate Protein Muffins

    5 from 2 votes
    Have your chocolate and eat it, too, with these high-protein muffins! They’re made with simple staples for a gluten-free and refined sugar–free breakfast or snack you can feel good about.
    Print Recipe Pin Recipe
    Prep Time 10 minutes mins
    Cook Time 15 minutes mins
    Total Time 25 minutes mins
    Servings: 12 muffins
    Course: Breakfast
    Cuisine: American
    Calories: 180
    Ingredients Method Nutrition Notes

    Ingredients
      

    • 1 ¾ cups oat flour (certified gluten-free, if needed)
    • ⅓ to ½ cup chocolate plant-based protein powder
    • 1 tablespoon cocoa powder
    • 2 teaspoons baking powder
    • ½ teaspoon baking soda
    • ¼ teaspoon kosher salt
    • ⅔ cup dairy-free milk alternative at room temperature
    • 2 eggs (at room temperature; see Egg-Free Option below)
    • ¼ to ⅓ cup maple syrup or honey
    • 3 tablespoons naturally refined coconut oil or avocado oil (see Oil Note below)
    • 1 teaspoon vanilla extract
    • ½ cup dairy-free dark chocolate chips

    Method
     

    1. Preheat the oven to 350°F (175°C). Line a 12-count muffin tin with liners or spray generously with cooking spray.
    2. In a mixing bowl, sift together the oat flour, protein powder, cocoa powder, baking powder, baking soda, and salt.
    3. In another large bowl, whisk together the milk alternative, eggs or banana, sweetener, oil, and vanilla.
    4. Gently combine the wet ingredients into the dry ingredients. Fold in the chocolate chips.
    5. Spoon the batter into the lined muffin pan, filling the cups two-thirds to three-quarters full.
    6. Bake the muffins for 15 to 18 minutes, or until a toothpick inserted into the center comes out clean. Remove from the oven and let cool in the muffin tin for 5 minutes. Remove the muffins to a cooling rack to finish cooling before serving.
    7. Store the muffins in an airtight container in the fridge for up to 1 week, or freeze for up to 3 months.

    Nutrition

    Serving: 1 muffinCalories: 180kcalCarbohydrates: 22.4gProtein: 8.4gFat: 7.6gSaturated Fat: 4.3gSodium: 169mgFiber: 2.8gSugar: 8.8g

    Notes

    Oil Note: If using coconut oil, use warm milk so the coconut oil won’t solidify. If using avocado oil, use milk at cold or room temperature.
    Egg-Free Option: Substitute 1 small banana, mashed, for the eggs.
    Vegan Option: Use maple syrup instead of honey and the egg-free option above.
    Credit: This recipe is reprinted with permissions and slightly adapted from The Gluten-Free Family Cookbook : Allergy-Friendly Recipes for Everyone Around Your Table by Lindsay Cotter.

    Tried this recipe?

    Let us know how it was!

    See Our Dairy-Free Protein Powder Guide for More Guidance!

    Share This!
    Alisa Fleming
    • Website

    Alisa is the founder of GoDairyFree.org, Food Editor for Allergic Living magazine, and author of the best-selling dairy-free book, Go Dairy Free: The Guide and Cookbook for Milk Allergies, Lactose Intolerance, and Casein-Free Living, and the new cookbook, Eat Dairy Free: Your Essential Cookbook for Everyday Meals, Snacks, and Sweets. Alisa is also a professional recipe creator and product ambassador for the natural food industry.

    8 Comments

    1. Emily on February 13, 2026 11:36 am

      Can I freeze these? If so, how long are they good in the freezer?

      Reply
      • Alisa Fleming on February 14, 2026 2:12 pm

        Yes, muffins freeze great! For best flavor, usually no longer than 2 to 3 months with muffins. You can reheat in the microwave, but they will taste much fresher if you can let them defrost at room temperature before eating.

        Reply
    2. Rebecca on September 11, 2025 6:50 am

      Can I use regular flour instead of oat flour?

      Reply
      • Alisa Fleming on September 11, 2025 11:44 am

        I haven’t tried this one with regular flour, but I think it would work. The batter should be somewhat thick (not runny like cake batter), but if it seems too thick, just stir in a little more milk alternative.

        Reply
    3. Whitney on July 9, 2024 1:00 pm

      5 stars
      Amazing, Incredible & Delicious sums up these muffins. The only thing I changed—vanilla beef Protien powder, skipped the vanilla. I added 1/4 cup cacao powder, used olive oil. Perfect breakfast, snacks, & post work out snack

      Reply
      • Alisa Fleming on July 9, 2024 4:43 pm

        That’s great! Thanks for sharing your modifications Whitney.

        Reply
        • Whitney on July 11, 2024 10:52 am

          5 stars
          I made a loaf of bread using your recipe with my modifications because it is what I have on hand and girl yum. The moisture of these muffins and the bread is unreal. It feels like we are eating a chocolate wheat cupcake or cake. Forever making this recipe

          Reply
          • Alisa Fleming on July 11, 2024 1:14 pm

            I’m glad it worked out!

            Reply
    5 from 2 votes
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