Made with whole wheat flour, naturally sweetened, and dairy-free, these Healthy Pumpkin Muffins are light, tender, perfectly spiced, and filled with delicious pumpkin flavor.

While these pumpkin muffins are on the healthier side, they do not sacrifice anything in flavor or texture.
Refined flour and sugar have been replaced with whole grains and natural sweeteners, yet these muffins are still light and tender. In fact, these pumpkin muffins are some of the moistest, most flavorful muffins I have ever had the pleasure of enjoying!
The secret to giving these whole wheat pumpkin muffins a delicate crumb is using both coconut milk and coconut oil. They work together to keep the muffins light and fluffy, and the slight flavor of coconut is the perfect match to the earthy undertones of the pumpkin.
While you may think that pumpkin muffins should be reserved for enjoying in the fall, these muffins are so delicious, that you will want to enjoy them year-round!
Healthier Ingredients

- Whole Wheat Flour: Instead of refined flour, these muffins are made with 100% whole wheat flour. I find this is one recipe that even people who aren't used to the heartiness of whole wheat flour enjoy. However, if you don't have whole wheat flour on hand, you can substitute all-purpose flour, white wheat flour, as well a gluten-free 1:1 flour blend.
- Coconut Milk: It is best to use canned coconut milk, not refrigerated coconut milk or canned coconut cream. While coconut milk is the secret to keeping these muffins super moist and light, this recipe will work if opt to use regular milk, almond milk, or buttermilk in place of coconut milk.
- Coconut Oil: Be sure to melt and cool your coconut oil so that it is in liquid form before adding it to the batter. You can sub out the coconut oil for canola oil or melted and cooled butter if desired.
- Honey: Instead of being sweetened with refined sugars, this recipe uses natural sweeteners. I typically opt for honey, but you can certainly use maple syrup in place of honey. Either option is delicious.
- Pumpkin Puree: Be sure to use 100% canned pumpkin or homemade pumpkin puree, not pumpkin pie filling. Pumpkin Pie filling is sweetened and spiced already and would not work in this recipe.
Step-By-Step Instructions
- Grease a muffin tin well with melted coconut oil or cooking spray or line with paper or silicone muffin liners.

- Sift together dry ingredients into a large mixing bowl. You could certainly, just whisk the dry ingredients together, but I do find sifting helps to prevent clumps of baking soda and baking powder in the muffins.

- In a separate bowl, mix together the coconut oil, egg, coconut milk, honey, and maple syrup until well combined. I always recommend mixing the wet ingredients together before adding the dry ingredients, as this helps keep the batter from getting overmixed.

- Combine wet and dry ingredients together using a spatula to fold the dry ingredients into the wet ingredients until everything is just moistened. You want to be careful not to over-mix the batter, to prevent these muffins from being tough or dense.

- Pour ¼ cup of muffin batter per muffin into prepared muffin tins. Pro-tip: Use an ice cream scoop to measure out the batter evenly and scoop it into the muffin cups without making a mess!

- Bake Pumpkin Muffins until just set. The best way to determine if your muffin is baked is to insert a toothpick into the center of the muffin, it should come out dry when the muffins are ready. No toothpick? Simply lightly touch the top of the muffin. It should spring back and not stick to your fingers.
- Allow the muffins to cool in the muffin tin for 5-10 minutes. Remove the muffins from the baking tin and cool fully before storing them.
- Enjoy one, or two, of these homemade pumpkin muffins. They are especially delicious when paired with a glass of warm Mulled Cider.

Storing Muffins
It is best to store these homemade pumpkin muffins in the fridge. Because they are made with whole grains, are super moist, and have no preservatives, they would potentially grow mold if left out at room temperature for longer than 24 hours.
Once cooled to room temperature, transfer the muffins to an airtight container and store them in the refrigerator for up to 5 days or freeze them in a freezer-safe container for up to 3 months.
Recipe Modifications
- Egg-Free Pumpkin Muffins: Use a flax egg in place of the egg in this recipe. Simply mix together 1 tablespoon ground flaxseed plus 3 tablespoons water and let sit for 5 minutes before adding to the batter.
- Vegan Pumpkin Muffins: To make these muffins vegan-friendly, use a flax egg in place of the egg and maple syrup in place of honey.
- Add Chocolate Chips: We love Pumpkin Chocolate Chip Muffins at our house! Add ½ cup of chocolate chips to the dry ingredients and toss before adding the wet ingredients. This will help the chocolate chips not sink to the bottom of the muffin. And be sure your chocolate chips are dairy-free if needed.
Recipe FAQs
There is a SLIGHT coconut undertone in the flavor of the muffins. If you don't like the flavor of coconut, I suggest replacing the coconut milk with almond milk and the coconut oil with canola oil, which still keeps these muffins dairy-free. If you are not dairy-free, you can use melted butter and regular milk.
Instead of using a pumpkin pie spice blend, I opt to use a combination of cinnamon, nutmeg, and ginger in this muffin recipe. I always have these spices on hand and therefore it is cheaper to use my own spices and I prefer to control the individual spices for the best flavor. If you have pumpkin pie spice mix on hand, omit the cinnamon, nutmeg, and ginger, and use 2 teaspoons of pumpkin pie spice blend in their place.
More Pumpkin Recipes
- Pumpkin Roll
- Healthy Pumpkin Bread
- Instant Pot Pumpkin Cheesecake
- Pumpkin Cake
- Homemade Pumpkin Pie
- Pumpkin Chocolate Chip Cookies
Whether looking for a dairy-free pumpkin muffin recipe, a healthy pumpkin muffin, or just a plain delicious Pumpkin Muffin, this is the perfect recipe! I would love to hear how you enjoy it in the comments below.

Healthy Pumpkin Muffins
Ingredients
- 2 ¼ cup whole wheat flour
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1 teaspoon salt
- 1 teaspoon cinnamon
- ½ teaspoon fresh nutmeg
- ½ teaspoon ground ginger
- 1 cup coconut milk
- 1 cup pumpkin
- 1 egg
- ½ cup coconut oil
- ½ cup honey or maple syrup
- 1 teaspoon vanilla extract
Instructions
- Preheat oven to 400 degrees F. Line a 12 cup muffin tin with liners or grease well with oil.
- Sift together flour, salt, baking soda, baking powder, nutmeg, cinnamon, and ginger over a large mixing bowl.
- In a separate bowl, mix together coconut milk, pumpkin, coconut oil, egg, honey, and vanilla extract.
- Add wet ingredients to dry ingredients and fold together gently, until just combined. Do not over mix.
- Measure about ¼ cup into each muffin cup.
- Bake for 15 minutes or until toothpick inserted in the center comes out clean.
- Cool for 10 minute in muffin tin and then carefully remove muffins and finish cooling on a wire rack.
Mm
This recipe was delicious I feel it could have used a little more spice but I really like this type of spice. Next time I think I'd add some grated ginger but overall this was an awesome recipe. I ended up doubling it to avoid having leftover pumpkin and coconut milk and I used butter because I already had some at room temperature. I missed the note about melting the butter and ended up throwing it in at a very soft room temperature which led to a lot of clumps so I put the whisk attachment on the hand mixer and beat the butter as small as I could before adding the dry ingredients. This led to small pockets of butter being found throughout the muffins and I imagine it would be the same with coconut oil, but that's not really a bad thing, finding a little pocket of butter was great.
E
These were a great way to use my garden pumpkins & they were excellent tasty muffins. I used coconut oil from a can, melted it, cooled it a little & dumped it into the liquids. I got a few big chunks of hardened oil almost immediately, I tried to break up the larger chunks and continued. Tried one, seems ok, not sure how the rest will b. Any explanations as to why I had this problem?
Kristen Chidsey
It sounds like your batter may have been cold when you added the oil, which will cause the warm oil to immediately harden. I would be sure everything else is at room temp to prevent this from happening. Glad you enjoyed the flavor.
Rachel
My favorite pumpkin muffin recipe! I've made it dozens of times with various milks, add-ins, and spices. They ALWAYS turn out amazing! Couple of my tips: add fresh ginger! It makes a HUGE difference. Melt the coconut oil before mixing so it's not lumpy. Dark chocolate chips make a nice addition and you don't need that many! Love, love, love this recipe.
Kristen Chidsey
Thanks so much for sharing your review AND your tips Rachel!
Michelle
Does 400° yield a fluffier muffin?
I baked them at 350° & curious how they might of been different. I love maple sweetened baked goods!
Thanks for creating these muffins!
Kristen Chidsey
Hi Michelle! I do find that baking at 400 degrees produces better results for this muffin. I have several recipes that I bake at 350 degrees or 375 with great results, but for this one, my tests resulted a more tender muffin when baked at 400.
Emily
Hi Kristen,
Would coconut butter work in lieu of coconut oil?
Emily
Kristen Chidsey
Hi Emily! I have not tried using coconut butter in place of the coconut oil, so I am not sure how that would change the consistency. I would imagine if melted, it would work well.
Emily
Thank you!
Maryanne
Made this recipe and as I pooped them into the oven and started cleaning up, I realized I forgot to add the egg! Even with that they still came out amazing! Added walnuts and some dried cranberries. Thank you for the recipe.
Kristen Chidsey
I am so glad these turned out despite the missing egg--that is a great thing for those with egg allergies to know 🙂
Alina Moro
Have you tried to make it gluten free?
Kristen Chidsey
I have made these with Bob's Red Mill 1:1 Gluten-Free Flour with success.
Beth
These are the perfect Fall treat!
Nellie Tracy
Delicious recipe! Love making this recipe for breakfasts!
Joanne
These were definitely moist but rather tasteless. Could double the spices and use chocolate chips. Will try again.
Kristen Chidsey
I am sorry you found these not flavorful enough for your tastes. My son does love these with chocolate chips.