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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. Sandra Knutson Avatar
    Sandra Knutson

    4 stars
    Every month I host a free Kids Paleo Pampered Chef Cooking Class where I teach the kids about healthy, organic, Paleo/GAPS/allergy friendly diet cooking. At my September Kids Paleo Pampered Chef Cooking Class I had 11 kiddos ages 6-12 years old and we made your Paleo Pumpkin Muffin and Bread recipe! We
    made 3 batches (1- mini muffin, 1- regular muffin size in my Brownie pan and 1 loaf). We just added Enjoy Life chocolate chips to ours. The recipe is so easy to make that the kids did 99% of it by themselves! I just read the recipe to them and put everything into the oven for them. They came out sooooo yummy! The kids devoured it all within 20 mins! Even the kids who have a hard time with food textures, colors or have never eaten anything that is grain free LOVED it and asked for seconds! Their parents were amazed that their children enjoyed it so much and were inspired to try exploring new and healthier food options at home with their “picky” kids. Yay! Thank you for sharing this super yummy recipe!

  2. Tammy Avatar

    My husband and I are huge fans of pumpkin pancakes. Has anyone tried making this recipe into a pancake recipe? What needs to be changed to make it work or pancakes?

  3. Ana Avatar

    Hi Katie,
    I Love your blog! And we have a very similar way to live life 🙂
    My son has some food allergies (milk protein – with consequence soya and beef, eggs, gluten and nuts).

    He doesn’t eat much (17 months) and he’s still breastfeed. He has a color changed in his front teeth, one first and after the 4! I was so concerned, take him to 2 dentists, they told it was demineralization, and that was nothing to do.

    Well I researched a lot, find de CTD group, bought the book, and find out that the cause was certainly the whole rice that I was using a lot!

    I’m changing that, but specially for breakfast and snacks I have a problem, what can I do that changes for the usually fruits and without eggs? I love your recipes, but there are so many eggs in there.

    Can you help me please?

    1. Karen Avatar

      5 stars
      Try duck eggs. People who are allergic to chicken eggs are not allergic to duck eggs.

  4. val Avatar

    4 stars
    Just made this with some (slight) changes/additions. I added a “pinch” of salt and a “handful” of good life chocolate chips which I chopped into smaller pieces to go further. The salt helps to bring out the flavor of the cinnamon, ginger and nutmeg in the pumpkin pie spice. And the chocolate, well that goes without saying! 🙂 I liked this recipe. I tried the Apple muffins first but they seemed a tad bland so I figured some salt might add some flavor.

  5. Judy Schweer Avatar
    Judy Schweer

    I have just started my attempt at restoring my teeth to better health. I use the Cod Liver gel supplement each day as well as a tablespoon of virgin coconut oil. My dentist said flossing is critical to keeping tooth decay at bay. I brush my teeth every night with a baking soda peroxide toothpaste before I go to bed. I am hoping that when I have my dental check up here in 4 months he will be pleased to see some improvement. I have always taken pretty good care of my teeth by find now as I am older after having children the task seems totally up hill. I am happy to be a member of this web site and look forward to the benefits.

  6. Christinere Avatar

    I love your recipe, but I am confused on something. Why is it so many of your recipes containing coconut oil say to back at 400 degrees? Isn’t coconut oil safe only up to 350 degrees? Or are you using refined coconut oil that is maybe safer for higher temps? Any clarification would be appreciated.

  7. April V Avatar

    So so so thankful for your site! Started our journey after discovering our middle child had many sensitivities including gluten and nuts and our youngest is corn allergic. Your site has made life so much more manageable and healthy too! Thanks for sharing SO many great tips!

    I tweaked this recipe to make it into healthy brownies by adding coco powder! Makes me feel like I’m not missing out too much! 🙂 (we eat it as written in the recipe too!)

    Thanks so much!

  8. Danielle Williams Avatar
    Danielle Williams

    This is so, so good, especially with the cream cheese in the middle. Yum! I will be making this often. It also freezes well after being cut into bars, and then thaws by lunch time when we take it for a sack lunch. Thanks for the recipe!

  9. Beth Avatar

    I made these as muffins, and while the flavor is good, the bottom of the muffins stuck horribly to the tins, despite a copious greasing with coconut oil.

    1. val Avatar

      Try using cupcake liners, worked out well and makes them more portable.

  10. Mary Avatar

    I recommend adding 1/2 teaspoon of salt to the batter. They are awesome! Thank you for making grain-free a yummy experience.

  11. Alex Avatar

    I made these and followed the recipe as it is listed. For the spices, I used 2 teaspoons of cinammon, 1/2 tsp each of cloves, nutmeg, and ginger. Then I added about 1/2 cup of good life chocolate chips and they were amazing!

  12. Trisha Williams Avatar
    Trisha Williams

    Ahhh!! I’m out of honey! Has anyone tried it with maple syrup??

  13. Ella Infj Avatar
    Ella Infj

    I have tried this recipe and 4 other recipes of yours and I give up. All taste disgusting!

    1. Gary Avatar

      5 stars
      Wow, what an insensitive and nasty thing to say. Try using a filter rather than write what awful things come to your mind first! Decorum and gracious “thanks but no thanks” go a long way.

    2. Kristin D Avatar
      Kristin D

      5 stars
      You are incredibly rude. Why waste your time and everyone else’s to leave a hateful comment? If you don’t like her recipes, QUIT MAKING THEM AND CREATE YOUR OWN.

  14. Drea Avatar

    I just tried this recipe and was pleasantly surprised by it. It was moist and spongy like a Yorkshire pudding. My whole family loved it! The non paleo eaters couldn’t even tell that there was no flour in it. It’s not very sweet but that’s because it’s bread not cake. Right? 😉 I followed the recipe exactly except for adding Chinese five spice with the cinnamon. I will definetly make this again.

  15. ashley Avatar

    Hello Katie. I’m wondering if I can use another flour instead of coconut flour for the pumpkin bread. I’m trying to use what I have on hand, I have an all purpose gluten free flour, or almond flour. thank you!

    1. Leanna Harter-Geer Avatar
      Leanna Harter-Geer

      Coconut flour requires a lot of egg and moisture so a substitution isn’t exactly possible. It would mean a pretty big rework of the recipe to use GF flour mix or almond flour. You’d actually probably be better off finding a grain pumpkin bread recipe that is low sugar or naturally sweetened and just directly subbing the GF flour mixture. 🙂

  16. Rose Avatar

    AAAAAkKKKKK HELP- I am new to baking with coconut flour, but I have to say that the batter was THICK so I thinned it to like a pasty muffin type batter.. So how much is enough and how much is to much?? Can you give a consitancy to aim for… I had to bake mine for 35 min_ just pulled the small loafs out and they seem like they may still be pasty… Any help would be appreciated. Thank You so much

    1. Wellness Mama Avatar
      Wellness Mama

      It will be thick… it should be spreadable but not pourable…

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