Whole Wheat Pumpkin Muffins

Breads and MuffinsDairy-FreeSnacks

By Kristen Chidsey

4.90 from 28 votes

Updated Sep 30, 2025

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These aren't your average pumpkin muffins. While fluffy, flavorful, and perfectly spiced, they are also naturally sweetened, dairy-free, and made with whole wheat flour.

If my family had to pick just one muffin to eat for the rest of our lives, we ALL would choose THESE whole wheat pumpkin muffins. They deliver soft, bakery-style results with wholesome ingredients and minimal prep.

A whole wheat, dairy-free pumpkin muffin cut in half to show how fluffy and soft inside of muffin is.

Kristen's Keys for Perfect Pumpkin Muffins

This pumpkin muffin recipe proves you CAN have it all! Dairy-free, refined sugar free, and 100% whole grains--and the very best pumpkin muffin you have ever had. But in order to achieve perfection, there are a few key things to keep in mind.

  • Use the right pumpkin. Stick with canned 100% pumpkin or well-drained homemade pumpkin puree. Pumpkin pie filling has added sweeteners and spices.
  • The whole wheat flour is interchangeable. This pumpkin muffin recipe is so forgiving. You can use whole wheat flour, whole white wheat flour, all-purpose flour, or even a 1:1 gluten-free flour.
  • Go for coconut. Using both canned coconut milk and melted coconut oil adds rich, nutty undertones that enhance the flavor of the pumpkin--without tasting like coconut. Plus it keeps these muffins dairy-free.

5-Star Reader Review

My favorite pumpkin muffin recipe! I've made it dozens of times with various milks, add-ins, and spices. They ALWAYS turn out amazing! --Rachel ⭐⭐⭐⭐⭐

How to Make Whole Wheat Pumpkin Muffins

Think of this step-by-step section as me in the kitchen helping you make fluffy, tender, delicious pumpkin muffins.

  1. Sift dry ingredients together. While you could certainly just whisk the dry ingredients together, I do find sifting the flour, baking soda, baking powder, salt, and spices best. That will ensure no unpleasant clumps of baking soda or baking powder.
Sifted and whisked whole wheat flour, baking soda, baking powder, salt, and spices together in mixing bowl.
  1. Combine wet ingredients. In a separate bowl, whisk together the pumpkin puree with the honey, coconut milk, egg, vanilla, and melted (and cooled) coconut oil.
Pumpkin puree, coconut milk, coconut oil, egg, and vanilla together in large mixing bowl.
  1. Combine. Using a spatula or wooden spoon, gently fold the wet ingredients into the dry, until just incorporated.

Don't Overmix

Stir just until the flour JUST disappears. Overmixing will activate the gluten, resulting in dense muffins.

Pumpkin muffin batter after dry and wet ingredients folded together in glass mixing bowl.
  1. Fill Muffin Cups. Use a ¼ cup measuring cup or ice cream scoop to portion out the matter into a greased or lined muffin tin. This will ensure the muffins bake evenly.
Ice cream scoop scooping pumpkin muffin batter into muffin tin.
  1. Bake. To keep these muffins soft and tender, bake until just set and toothpick inserted into the center of the muffin comes out dry.

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.

Recipe Modifications

  • No Honey? Feel free to swap honey for pure maple syrup.
  • Egg-Free: Combine 1 tablespoon of ground flaxseed with 3 tablespoons of water and use in place of the egg.
  • Chocolate Lover? Add ½ cup chocolate chips to the dry ingredients for the best Pumpkin Chocolate Chip Muffins.
  • No Coconut Milk? Sub with your favorite non-dairy milk or regular milk if you aren't dairy-free.
  • Coconut Oil Substitution: Use canola oil or if not dairy-free, melted and cooled butter.

Note on Yield and Storage

As written, this recipe yields 12 glorious, fluffy whole wheat pumpkin muffins. And as true for moist, whole wheat baked goods, storing in the fridge is key to preventing mold growth.

  • Yield: This recipe calls for 1 cup of pumpkin puree, which is half of one 15 ounce can. While I strongly recommend doubling the recipe, as these pumpkin muffins are just so irresistibly good and they freeze exceptionally well, you can also opt to make another recipe calling for pumpkin puree. Maybe pumpkin pasta for something new and unexpected or compliment your muffin with a Homemade Pumpkin Spice Latte?
  • Storage: Cool completely, then store in an airtight container in the fridge for up to 5 days or freeze in a freezer-safe bag or container for up to 3 months.

More Baked Goods with Pumpkin

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4.90 from 28 votes

Whole Wheat Pumpkin Muffins

By: Kristen Chidsey
Servings: 12
Prep: 5 minutes
Cook: 15 minutes
Total: 20 minutes
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A dairy-free, naturally sweetened, whole wheat pumpkin muffin cut in half to show how fluffy and soft inside of muffin is.
Made with whole wheat flour, naturally sweetened, and dairy-free, these Pumpkin Muffins are light, tender, perfectly spiced, and filled with delicious pumpkin flavor.

Video

Ingredients 

  • 2 ¼ cups whole wheat flour, or all-purpose flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1 teaspoon kosher salt
  • 1 teaspoon ground cinnamon
  • ½ teaspoon grated nutmeg
  • ½ teaspoon ground ginger
  • 1 cup coconut milk, or almond milk
  • 1 cup 100% pumpkin puree
  • 1 large egg
  • ½ cup coconut oil, melted, and cooled
  • ½ cup honey, or maple syrup
  • 1 teaspoon vanilla extract

Instructions 

  • Preheat oven to 400℉ (200℃). Line a 12-cup muffin tin with liners or grease well with oil.
  • Over a large mixing bowl, sift 2 ¼ cups whole wheat flour, 1 teaspoon baking powder, 1 teaspoon baking soda, 1 teaspoon kosher salt, 1 teaspoon ground cinnamon, ½ teaspoon grated nutmeg, and ½ teaspoon ground ginger Whisk to combine ingredients.
    Sifted and whisked whole wheat flour, baking soda, baking powder, salt, and spices together in mixing bowl.
  • In a separate bowl, mix together 1 cup coconut milk, 1 cup 100% pumpkin puree, 1 large egg, ½ cup coconut oil, ½ cup honey, and 1 teaspoon vanilla extract together until well combined.
    Pumpkin puree, coconut milk, coconut oil, egg, and vanilla together in large mixing bowl.
  • Add wet ingredients to dry ingredients and fold together gently, until just combined. Do not over-mix as this will result in dense muffins.
    Pumpkin muffin batter after dry and wet ingredients folded together in glass mixing bowl.
  • Measure about ¼ cup into each muffin cup, until each muffin cup is about ¾ of the way full.
    Ice cream scoop scooping pumpkin muffin batter into muffin tin.
  • Bake for 13-15 minutes or until a toothpick inserted in the center comes out clean.
    Baked Pumpkin muffins in silver muffin tin on cooling rack.
  • Remove the muffins from the oven and let them cool for 10 minutes in the muffin tin on a cooling rack. After 10 minutes, carefully remove the muffins from the tin and finish cooling on a wire rack.
    Three Healthy Pumpkin Muffins on blue plate with nutmeg and coconut in background.

Equipment

Notes

Coconut Milk: Swap out buttermilk, regular milk, or your favorite non-dairy milk. 
Coconut Oil: Use canola oil or melted and cooled butter in place if desired.
Flour: Whole white wheat, all-purpose flour, or an all-purpose 1:1 gluten-free flour can be used in place of whole wheat flour.
Spices: Feel free to use 2 teaspoons of homemade pumpkin pie spice in place of the cinnamon, nutmeg, and ginger. 
Pumpkin: Use canned or homemade pumpkin puree, not pumpkin pie filling. If using homemade puree, strain over a fine-mesh strainer lined with cheesecloth for 2-4 hours and then measure out 1 cup of the strained puree to use for the muffins. 
Egg-Free: Mix together 1 tablespoon of ground flaxseed plus 3 tablespoons water and let sit for 5 minutes before adding to the batter in place of egg.
Add Chocolate Chips: Add ½ cup of chocolate chips to the dry ingredients and toss before adding the wet ingredients.
Double the Recipe: I recommend doubling this recipe to put a full 15 ounce can of pumpkin puree to use. These pumpkin muffins freeze well, so doubling the recipe is never a bad idea.
Storage: Store muffins in the fridge in an airtight container for up to 5 days and in the freezer for up to 3 months. These pumpkin muffins are so moist, they would mold if left out at room temperature.

Nutrition

Calories: 207kcalCarbohydrates: 28gProtein: 3gFat: 10gSaturated Fat: 8gCholesterol: 13mgSodium: 291mgPotassium: 160mgFiber: 2gSugar: 12gVitamin A: 845IUVitamin C: 0.9mgCalcium: 29mgIron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Tried this recipe?Mention @amindfullmom or tag #amindfullmom!

About Kristen Chidsey

Kristen is a wife, busy mom of two, and creator of A Mind "Full" Mom. From breakfast to dinner to dessert, it is her passion to share tried-and-true recipes that are big on flavor, made with easy-to-find ingredients, and family-approved!

Read More About Me

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59 Comments

  1. Yum! These look good! Perfect way to start the day or even a healthy snack! Thanks for linking them up with us at Foodie Fridays!

    Reply

  2. 5 stars
    I would just love one of your Whole Wheat Pumpkin Muffins right now! Hope you are having a great day and thanks so much for sharing this awesome post with Full Plate Thursday.
    Come Back Soon!
    Miz Helen

    Reply

    1. Miz Helen, You will love them!! I have had a stomach bug the past week and no appetite. Today was the first day I woke up with any appetite and I immediately grabbed a muffin from the freezer and sunk my teeth into it. YUM!

      Reply

    1. Jennie, You must have been commenting when I was sharing my recipe at Friday Favorites. I love your link up party! Enjoy the muffins--they are tasty!

      Reply

  4. I've been on the hunt for some dairy-free pumpkin recipes, and these look fantastic! I definitely cannot wait to try them out. Stopping by from the Wonderful Wednesday Blog hop, and pinning this recipe!

    Reply

    1. Yea!! Bev, I am so happy to deliver this recipe to you. The coconut products add such a subtle richness..you will love them!

      Reply