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.

Filled with pumpkin puree and warming pumpkin spice flavor, these pumpkin muffins are an obvious treat for fall. But after one bite of these rich, soft pumpkin muffins, you will want to enjoy them year-round.

Healthy Pumpkin Muffin on wooden cutting board.

what makes these pumpkin muffins the best

Insanely Delicious. The coconut milk, coconut oil, cinnamon, ginger, and nutmeg all work to complement the earthy undertones of the pumpkin.
Whole Grain. This pumpkin muffin recipe is made with 100% whole wheat flour, adding fiber and nutrients to the muffin.
Light & Fluffy. Even though these muffins are made with whole wheat flour, they are not at all dense or dry. In fact, these muffins are some of the moistest muffins I have ever enjoyed.
Naturally Sweetened. Instead of being made with refined sugar, these pumpkin muffins are sweetened with honey.
Healthy Pumpkin Muffin Recipe. Because these muffins are made with whole grains, naturally sweetened, and loaded with vitamin-rich pumpkin puree, these pumpkin muffins may taste as rich and decadent as a slice of pumpkin pie or pumpkin cake, yet they are actually suitable for enjoying as part of a healthy breakfast.

Notes on Ingredients

Ingredients for dairy-free pumpkin muffins labeled on white counter.

Whole Wheat Flour: Instead of using all-purpose 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 or white wheat flour in place of whole wheat flour if desired.
Coconut Milk: It is best to use canned coconut milk, not refrigerated coconut milk or canned coconut cream. While coconut milk is one of the ingredients that help to keep these pumpkin 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 substitute 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.
Spices: These muffins are made with ground nutmeg, ground cinnamon, and ground ginger, which gives them just the right warming flavor. However, if you love the classic flavor of pumpkin spice, feel free to use pumpkin pie spice blend.
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.

Substitutions & Modifications

Egg-Free Pumpkin Muffins: Use a flax egg in place of the egg in this recipe. Simply mix together 1 tablespoon of ground flaxseed plus 3 tablespoons water and let sit for 5 minutes before adding to the batter.
Gluten-Free Pumpkin Muffins: Use an all-purpose 1:1 gluten-free flour blend in place of the whole wheat muffins.
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.
Coconut-Free Pumpkin Muffins: There is a SLIGHT coconut undertone in the flavor of the muffins. If you don't like the flavor of coconut or have an allergy to 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.

Tips for the Best Healthy Pumpkin Muffins

This recipe for pumpkin muffins comes together easily and you will find the detailed instructions in the recipe card. However, I do want to walk you through a few expert tips to ensure that your healthy pumpkin muffins turn out fluffy, moist, and delicious.

Tip #1: Sift dry ingredients together. While you could certainly just whisk the dry ingredients together, I do find sifting helps to prevent clumps of baking soda and baking powder in the muffins.

Dry ingredients for pumpkin muffins in sifter over mixing bowl.

Tip #2 Don't over-mix the batter. Fold the batter together using a spatula or wooden spoon, until no pockets of flour remain. Just keep in mind to not overmix your muffin batter, as this activates the gluten in the flour, and will cause your muffins to be tough.

Tip#2: Combine wet ingredients in a separate bowl. Mixing the wet ingredients together before adding the dry ingredients, as this helps keep the batter from getting overmixed.

Pumpkin puree, egg, and coconut milk in mixing bowl.

Tip #3: Gently Mix Batter. Combine wet and dry ingredients together using a spatula to fold the dry ingredients into the wet ingredients until everything is moistened. You want to be careful not to over-mix the batter, to prevent these pumpkin muffins from being tough or dense.

Pumpkin muffin batter in glass mixing bowl.

Tip #3: Evenly divide the muffin batter. I have found that it is best to use an ice cream scoop or ¼ cup measuring cup to scoop out the batter. This will keep each muffin the exact same size, which means they will bake evenly.

Ice scream scoop scooping muffin batter into muffin tin.

Tip #4 Don't overbake the muffins. To keep these pumpkin muffins soft and tender, bake them until they are 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.

Baked Pumpkin muffins in silver muffin tin on cooling rack.

How to Store Whole Wheat Pumpkin Muffins

Because these healthy pumpkin muffins are made with whole grains, super moist, and preservative-free, they will quickly mold if stored at room temperature. It is best to allow the baked pumpkin muffins to cool to room temperature and then store the muffins in an airtight container in the refrigerator for up to 5 days.

Alternatively, you can store the cooled pumpkin muffins in a freezer-safe container for up to 3 months.

More Favorite Pumpkin Baked Goods

Whether looking for a dairy-free pumpkin muffin recipe, a healthy pumpkin muffin, or just a canned pumpkin recipe, this is the perfect recipe! I would love to hear how you enjoy it in the comments below.