Gluten-Free Almond-Butter Pumpkin Muffins with a Cocoa Swirl

Everyone loves a hearty muffin, right? However, when you are eating healthily, and especially if you have food allergies, finding a truly healthy and safe muffin can be a real dilemma.

Muffins are similar to a cupcake, but without the frosting. They often have fruit, which adds to their nutritional quotient, but the problem is, many (especially those in coffee shops and restaurants) have more sugar than a piece of cake or a candy bar. Luckily, you can make your own healthy muffins at home with simple ingredients.

The recipe below will yield 24 muffins that freeze well, are portable, and are incredibly moist and flavorful! 

Tips on allergen-free baking

The key to making allergen-free goodies taste great is to carefully choose gluten-free flours to replace flour that contains gluten. Choosing a good ingredient to replace eggs is also key if you have an egg allergy.

Here are the top nine most common allergens:

  • Soy
  • Dairy
  • Gluten
  • Wheat
  • Shellfish
  • Eggs
  • Sesame
  • Tree nuts
  • Peanuts

Of these, gluten, wheat, and dairy are the most allergenic, with eggs and peanuts being a close second. When baking muffins for yourself or others, it’s often a good idea to make them allergen-free, just in case you (or your guests) have a sensitivity you aren’t aware of.

Baking without gluten

When you remove the gluten from a recipe, you’re eliminating part of the glue that holds baked goods together. Gluten is also one of the reasons baked goods rise so well. But not to worry, adding a teaspoon each of baking powder and baking soda is all you need to help gluten-free baked goods rise. You can also use other natural ingredients to help bind your recipes (more on this below).

When eliminating gluten and wheat-based flours, you’ll need to choose a blend of gluten-free flours for the best results. However, I’m not a fan of gluten-free flour mixes — most are made from white rice or tapioca/potato starch, which are very low in nutrients. I use a mix of gluten-free oat flour and coconut flour, which works just great, and tastes much better, too!

I also add cocoa powder to these muffins. The acidity in the cocoa reacts with the baking soda and baking powder to make the goods rise even more, and it makes them light and fluffy. Cocoa powder is also full of antioxidants, and it can replace some of the flour in any baking recipe.

Egg-free baking

octAbtGWhen you eliminate eggs, you’re also eliminating a natural binder and raising agent all in one. Instead of egg replacement products (such as powders), I prefer to use applesauce, apple butter (no sugar added), pumpkin, banana, or puréed prunes (yes, really). These ingredients are moist and flavorful, and including them allows you to omit the oil and reduce the sweetener in a recipe.

Almond butter can also be used in place of eggs. Nut butter adds moisture and depth, and helps the muffins stay together. It also adds that flavor, fiber, and vitamin E. However, if you have a tree nut allergy, you can use sunflower seed butter in place of nut butter for the same results and flavor.

About this muffin recipe

Gluten-Free Almond-Butter Pumpkin Muffins
Prep Time:
Cook Time:
Total time:
Recipe by:The Alternative Daily
These muffins incorporate some of fall’s finest ingredients, along with some especially indulgent (yet healthy) flavors like coconut and chocolate. They are grain-free, vegan, gluten-free, and completely free of sugar. If you don’t want to use pumpkin or applesauce, you can use banana, puréed prunes, or carrots instead. Makes 24 Muffins (or 1 dozen muffins and 1 large loaf cake)
  • 1/3 cup coconut flour
  • 1/3cup gluten-free oat flour
  • 1/3cup ground flax seed
  • 1/4cup Dutch (dark, alkalized) cocoa powder
  • 1teaspoon each of aluminum-free baking powder and baking soda
  • 1teaspoon cinnamon
  • 1tablespoon of ground chia seeds (or more flax)
  • 1/2cup shredded coconut (optional, but adds flavor)
  • 1tablespoon ground vanilla beans (or you can use pure vanilla extract in the liquid ingredients)
  • 1full teaspoon of ground stevia leaves (not processed stevia powder)
  • 2/3cup unsweetened almond milk (or your choice of milk)
  • 2/3cup water
  • 1tablespoon pure vanilla extract (if you didn’t use the ground vanilla above)
  • 1/4cup plain almond butter
  • 1can of pumpkin purée
  • 1/2cup unsweetened apple butter or applesauce
Servings: Muffins
  1. Preheat the oven to 350 degrees Fahrenheit.
  2. In a large bowl, mix the dry ingredients together until they are thoroughly blended.
  3. In a separate bowl, mix all of the liquid ingredients together. Add to the dry ingredients slowly, stirring as you go. The coconut and flax will cause the mixture to thicken quickly, so keep stirring until you see no more bits of flour. It should resemble a muffin batter consistency. You can also use a blender for this step.
  4. You’ll notice that the batter has swirls of orange and brown, thanks to the pumpkin and cocoa. I like to leave my batter like this, so the muffins look especially seasonal when they’re baked!
  5. Grease a muffin pan and a loaf pan with some coconut oil. Scoop the batter into each of the muffin cups and the loaf pan until they are three-quarters of the way full.
  6. Bake for 45 minutes or until firm on top and lightly golden brown.
  7. Remove from the oven and let the muffins and loaf cool in the pan for at least 1 hour away from the stove.
  8. Use a gentle casing knife to pry the muffins out. Serve warm, or refrigerate them to enjoy all week!
Recipe Notes

*You can also freeze these muffins individually and thaw for 30 minutes on the counter to enjoy for breakfast or a healthy snack!

Serving suggestions:

If you like, you can spread a muffin with apple butter, almond butter, a homemade jam, or even a little coconut butter. Be sure to enjoy these muffins with a hot cup of coffee — they really hit the spot!


If you have a food allergy, don’t be afraid to experiment with your own homemade goodies. They’re much healthier than store-bought options that have added sugars and chemicals. If you have an allergen-free recipe you love and make regularly, what tips and ingredient suggestions do you have to share?

—Heather McClees

Heather McClees is a professional health journalist and Certified Holistic Nutritionist from South Carolina. She received her B.S. Degree in Nutrition Science and Dietetics, and is most passionate about helping others discover the gift of of holistic health, showing others how to create healthy recipes based on their favorite foods, physical fitness and yoga, and creative writing.


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