Healthy Pumpkin Muffins (Dairy-Free Recipe)

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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.

Healthy Pumpkin Muffin on wooden cutting board.

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

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

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.

Muffin Liners in muffin cup with pumpkins in background.

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.

Dry ingredients for pumpkin muffins in sifter over mixing bowl.

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.

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

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.

Pumpkin muffin batter in glass mixing bowl.

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!

Ice scream scoop scooping muffin batter into muffin tin.

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.

Baked Pumpkin muffins in silver muffin tin on cooling rack.

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

Do these pumpkin muffins have the flavor of coconut?

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.

Why no Pumpkin Pie Spice?

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

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.