October 12, 2017

Pumpkin Muffins with Chocolate Chips (Gluten-Free, Dairy-Free)

Last Updated on September 17, 2025 by Carrie Korem, FNTP

There’s nothing better than a batch of warm pumpkin muffins on a crisp fall day. These pumpkin muffins are made with coconut flour, sweetened naturally, and dotted with chocolate chips for a treat that feels indulgent yet still supports your health. The texture is light and tender, and they’re perfect to enjoy for breakfast, as an afternoon snack, or tucked into lunchboxes.

I especially love this pumpkin muffins recipe because it uses simple, whole ingredients — no grains, no refined sugars, and dairy-free options if you need them. They store well on the counter for a few days and can be frozen, which makes them great for meal prep.

Why Bake Pumpkin Muffins with Coconut Flour?

Coconut flour can be tricky, but once you know how it works, you’ll love using it for baking:

Moisture matters: Coconut flour soaks up a lot of liquid. That’s why this pumpkin muffins recipe calls for several eggs. Without enough moisture, coconut flour baked goods can turn out dense.
Stick to one brand: Different brands of coconut flour can give very different results. I always use Bob’s Red Mill coconut flour for consistent texture.
Pair with almond flour: Often, coconut flour works well with almond flour to keep muffins soft while using fewer eggs.
Choose the right sweetener: For a lighter texture, I recommend using dry sweeteners like coconut sugar or maple sugar instead of liquid ones.

How to Make Pumpkin Muffins

Making these muffins is simple and doesn’t take much time. You’ll whisk the wet and dry ingredients and then fold everything into the pumpkin puree and chocolate chips. A quick bake in the oven, and you’ve got fluffy, delicious pumpkin muffins ready to enjoy.

Here’s the recipe:

Ingredients

6 large eggs
1/3 cup heavy cream (or coconut milk for Paleo)
1/4 cup + 2 tablespoons coconut sugar or maple sugar
1 teaspoon vanilla extract
8 tablespoons unsalted butter, melted (or coconut oil for dairy-free)
3/4 cup coconut flour
2 teaspoons grain-free baking powder (1 part baking soda + 1 part cream of tartar + 2 parts arrowroot)
1 teaspoon baking soda
3/4 teaspoon Celtic sea salt
1 cup cooked and pureed pumpkin
5 ounces mini chocolate chips or chopped dark chocolate

Instructions

Preheat the oven to 400°F. Line a muffin pan with muffin liners.
In a large bowl, whisk together the eggs, cream (or coconut milk), coconut sugar, vanilla, and butter.
In another bowl, sift the coconut flour, baking powder, baking soda, and salt. Add the dry ingredients to the wet and whisk until smooth.
Fold in the pumpkin puree and chocolate chips.
Spoon the batter into muffin cups and bake for 15 minutes, or until golden brown on top.

Variations

Leave out the chocolate and add pecans, walnuts, or white chocolate chips instead.
For a nutty flavor, try adding a sprinkle of chopped nuts on top before baking.
Enjoy them plain for a naturally sweet and simple muffin.

Pumpkin is rich in beta-carotene, fiber, potassium, and antioxidants that support your thyroid and overall health. Paired with healthy fats and protein in this recipe, these pumpkin muffins are more than a seasonal treat — they’re a nourishing choice you can feel good about.

Here are some other muffin recipes you’ll enjoy!

Browned Butter Banana Muffins with Cinnamon Streusel
Fermented Sourdough Banana Zucchini Muffins
Blueberry Streusel Muffin
Lemon Poppy Seed Muffins