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Grain-Free Healthy Pumpkin Muffins and Bread

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Wellness Mama » Blog » Recipes » Grain-Free Healthy Pumpkin Muffins and Bread

 Ahh, fall… the glorious season of apples, pumpkins, changing leaves, and cooler weather (finally!). I definitely get in on the fall pumpkin craze and start making pumpkin spice everything this time of year. This coconut flour healthy pumpkin muffins (and bread) recipe is the perfect way to ring in the season.

Healthy Pumpkin Muffins (and Bread!)

Unlike most baked goods, these delicious muffins are a great low-sugar snack or breakfast. Instead of refined sugar or brown sugar, they use natural sweeteners, like honey, stevia, or maple syrup. They’re also packed with plenty of protein, fiber, and healthy fats. Slather some grass-fed butter on the top and they make the perfect yummy fall breakfast.

Perfect Paleo Pumpkin Bread

If this is your first time baking grain-free bread, expect a denser bread or muffin. They’re still moist with a soft texture and all the warm flavors of pumpkin spice (with just the right touch of sweetness).

Instead of all-purpose flour, white whole wheat flour, or even whole wheat flour, these muffins rely on coconut flour. I use this a lot to bake with in my grain-free recipes. Whole grains are often a staple in healthier muffin recipes, but it’s not something our family eats much of.

Since coconut flour can vary, if your batter ends up way too thick, then add a little bit of milk to thin it. Some muffin recipes replace the butter or coconut oil with applesauce. I haven’t personally tried it here, but let me know if you do!

Pure Pumpkin Flavor

You can use homemade pumpkin puree or a can of pumpkin for these. They’re delish either way! Just be sure to not get the can of pumpkin pie filling at the store instead of pure pumpkin. While the filling already has added spices, it also has lots of added refined sugar.

Even though pumpkin has become a staple in fall cooking it’s worth having all year round. Pumpkin is high in vitamin A (the beta-carotene version), vitamin C, and potassium. There’s nothing quite like biting into some warm pumpkin bread or muffins!

The healthy pumpkin muffins are delicious by themselves or with a little melted butter or coconut oil. This recipe also freezes well once baked if you prefer to batch cook.

Healthy Pumpkin Muffin Variations

  • Add in some dark chocolate chips, chopped nuts, or dried cranberries to the batter.

  • Top with a dollop of raw milk or coconut whipped cream.

  • If you eat dairy, you can pour half of the batter into an 8×8 pan, add slices of cream cheese, and then add the rest of the batter.

  • We also mix it up and use a similar coconut flour base recipe to make grain-free banana bread or apple cinnamon muffins.

Need an egg-free version? Try making the muffins with flax eggs, made with ground flaxseed and water mixed together. Here’s how to substitute eggs in recipes like cupcakes, muffins, and more.

If you are looking for a grain-free, low-carb, and sugar-free bread for breakfast or dessert … try this recipe! It just might become a new favorite.


Healthy Pumpkin Muffins Recipe

Simple gluten-free, dairy-free, and grain-free pumpkin muffins made with coconut flour, warm spices, and pumpkin for a healthy and nutritious breakfast. Can also be made as healthy pumpkin bread.
Prep Time 5 minutes
Cook Time 20 minutes
Total Time 25 minutes
Calories 139kcal
Author Katie Wells


12 muffins (or 1 loaf)



  • Preheat oven to 400°F.
  • Lightly grease muffin tins (or use paper muffin liners) or an 8×8 baking dish with coconut oil or olive oil. A regular loaf pan doesn't work well.
  • Put all ingredients in a medium-sized bowl and mix with an immersion blender or strong whisk until smooth and well incorporated. If the batter is too thick, add a little coconut milk, almond milk, or water to thin, but don’t let it get runny at all.
  • Scoop into greased muffin cups with a ¼ cup measure or pour into a greased 8×8 baking dish. 
  • Bake for 13-18 minutes for a muffin pan or 20-25 minutes for bread. Cook until lightly browned and set in the middle (a toothpick inserted in the middle should come out clean).


Nutrition Facts
Healthy Pumpkin Muffins Recipe
Amount Per Serving (1 muffins)
Calories 139 Calories from Fat 68
% Daily Value*
Fat 7.6g12%
Saturated Fat 5.8g36%
Cholesterol 68mg23%
Sodium 131mg6%
Carbohydrates 14.6g5%
Fiber 4.7g20%
Sugar 6.7g7%
Protein 3.9g8%
* Percent Daily Values are based on a 2000 calorie diet.


Optional: Finely grind almonds or pecans and mix with butter or coconut oil to make a crumble topping.
Store the healthy pumpkin muffins in an airtight container at room temperature. 

Like this recipe? Check out my cookbook, or get all my recipes (over 500!) in a personalized weekly meal planner here!

What’s your favorite way to eat pumpkin? What mix-ins do you like adding to your muffins? Leave a comment and let me know!

Katie Wells Avatar

About Katie Wells

Katie Wells, CTNC, MCHC, Founder of Wellness Mama and Co-founder of Wellnesse, has a background in research, journalism, and nutrition. As a mom of six, she turned to research and took health into her own hands to find answers to her health problems. WellnessMama.com is the culmination of her thousands of hours of research and all posts are medically reviewed and verified by the Wellness Mama research team. Katie is also the author of the bestselling books The Wellness Mama Cookbook and The Wellness Mama 5-Step Lifestyle Detox.


165 responses to “Grain-Free Healthy Pumpkin Muffins and Bread”

  1. Diane Avatar

    5 stars
    Followed recipe exactly as printed for an 8×8, with finely chopped pecans in warmed coconut oil as a topping. Reviewer comments prompted me then to add a light drizzle of maple syrup (used honey only in batter) and a sprinkling of flaky salt over the nutty surface. The resulting bake was lovely, satisfying, well received, and I shall make again. Thank you, Katie.

  2. Mary Avatar

    5 stars
    My kids like these muffins. I usually add some chocolate chips and 1/4 tsp salt. I highly recommend using the spice amounts listed in the recipe – I use 1 Tbsp. ground cinnamon plus other complementary spices (1/2 tsp. ground ginger, 1/4 tsp. ground cloves, 1/4 tsp. ground nutmeg or ground mace, and sometimes a sprinkle of cardamom). I keep coming back to this recipe because these are more filling than regular flour muffins and also because the recipe is simple and quick to make.

  3. Valerie Avatar

    5 stars
    Really love these & so do my kids! Great source of quick protein in the morning or as a snack.
    How long would they keep in the fridge?

    Thank you

  4. Catherine Avatar

    5 stars
    These are fabulous and perfect fall flavors. I also love how they’re basically guilt-free. My only qualm is that mine didn’t rise like the photo and were dense and more flat (still didn’t mind!) but did I miss something? Anyone else have this issue?

  5. Nina Avatar

    5 stars
    Made these this morning and added a pinch of pink salt and chopped walnuts. YUM! I’m not a sweet person, but these were pretty sweet to me – not sure what others are talking about! I’m also not the hugest fan of coconut flour as every recipe I’ve tried leaves goods dry as heck – these muffins are super moist and I love all the protein from the eggs. Awesome savory breakfast option with coffee – will be making these all winter!

  6. Daniela Avatar

    4 stars
    Followed this recipe but used a pure quality honey. I believe that makes the difference. If you want a kick at chocolate chips to the recipe, nuts or coco nibs or finish it off with a little Nutella…. you will be good to go.

  7. Dee Avatar

    5 stars
    These muffins are great! I added 1/4 teaspoon allspice, a 1/4 cup Lily’s chocolate chips, 1/8 cup sunflower seeds and subbed sugar free maple syrup for the honey. So good! I also frosted some of the muffins with a low carb cream cheese frosting. What a treat! Reminded me of the Spanish bar cakes I had growing up.

  8. Lynnsey Avatar

    Hi Katie. New to giving up wheat… this recipe tasted delicious, but came out rather flat, extra dark brown, and crazy moist. The same thing happened with your coconut flour biscuits. I live in high altitude. With wheat recipes I increase flour, decrease sugar, and increase moisture. Got any suggestions? Thanks for the recipe and great info!

  9. Melanie Avatar

    I have made these several times and they are outstanding!So nice to be eating delicious grain free! Taste like a real treat!

  10. Danielle Avatar

    I’ve been playing off this recipe for awhile now and wanted to say thanks. It’s been a life saver with my MS. Some days I’m too tired to eat and if I have a batch of these I know I’ll at least get something in me.
    My base is a shy 1/2c coconut with a few pinches of arrowroot to top it off. I prefer a little mix. I have used agave, maple and honey. I like agave the best and can get away with 2-3 TBS I use the immersion blender and it gets light and fluffy and airy and then I always add in some unsweetened almond milk to thin it to the right texture.

    I’ve done grated carrots, Apple, zucchini etc for more bulk and walnuts on top that get extra toasty so it’s overall more like a morning glory muffin.
    I eat these for breakfast and have no guilt. I love that it uses a lot of eggs because I have chickens and there’s only so many frittata muffins I can eat.

  11. Adinda Avatar

    5 stars
    This recipe is insane! Best low-carb bread/cake I’ve eaten so far. Thanks a million 🙂

  12. Sarah Avatar

    I made this recipe and I made it in a loaf pan. I covered it with foil and baked for 45 min and it came out perfect!

  13. Vanessa Avatar

    Hi, I have made this recipe multiple times and I really enjoy it. I now have the need to be egg-free in addition to dairy and gluten free for health reasons. I tried it once with chia eggs and it didn’t turn out well. I can’t use flax. Any tips on how to make chia eggs work in this recipe? Thank you!

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