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    Healthy Pumpkin Muffins

    Breads and Muffins Dairy-Free Recipes Snacks September 25, 2023 | By Kristen Chidsey | 55 Comments | *This post may contain affiliate links. Read my disclosure policy.

    Jump to Recipe
    These are the BEST healthy pumpkin muffins out there! Even though this recipe uses all whole wheat flour, maple syrup, and is dairy-free, these pumpkin muffins are light, moist, tender, and perfectly spiced. They are the best from-scratch EASY muffin recipe to satisfy that pumpkin spice craving!

    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

    • Pumpkin Roll
    • Pumpkin Cream Cheese Bread
    • Pumpkin Cake
    • Pumpkin Banana Muffins
    • Pumpkin Baked Oatmeal
    • Homemade Pumpkin Pie
    • Pumpkin Chocolate Chip Cookies

    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. 

    Baked Whole Wheat Pumpkin Muffins on wooden cutting board

    Healthy Pumpkin Muffins

    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.
    4.89 from 26 votes
    Print Pin Rate
    Course: Snack
    Cuisine: American
    Prep Time: 5 minutes minutes
    Cook Time: 15 minutes minutes
    Total Time: 20 minutes minutes
    Servings: 12
    Calories: 207kcal
    Author: Kristen Chidsey

    Ingredients

    • 2¼ cups whole wheat flour or all-purpose flour
    • 1 teaspoon baking powder
    • 1 teaspoon baking soda
    • 1 teaspoon 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
    Prevents your screen from going dark while preparing the recipe.

    Instructions

    • Preheat oven to 400℉. 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 and then whisk to combine ingredients.
      Ingredients for pumpkin muffins being sifted together in fine mesh strainer.
    • 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 as this will result in dense muffins.
      Pumpkin muffin batter mixed together in clear mixing bowl.
    • Measure about ¼ cup into each muffin cup, until each muffin cup is about ¾ of the way full.
      Scoop measuring out pumpkin muffin batter evenly into lined muffin tin.
    • Bake for 15 minutes or until a toothpick inserted in the center comes out clean.
      Baked Pumpkin Muffins in 6 cup muffin tin with nutmeg and coconut off to side
    • 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.

    Equipment Needed

    • muffin tin
    • muffin cup liners

    Notes

    Coconut Milk: In place of coconut milk, feel free to use buttermilk, regular milk, or your favorite non-dairy milk. 
    Coconut Oil: In place of coconut oil, melted and cooled butter may be used, as well as canola oil. 
    Flour: Whole white wheat/all-purpose flour also works in place of whole wheat flour. Alternatively, use an all-purpose 1:1 gluten-free flour blend to keep these muffins gluten-free.  
    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. 
    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: 207kcal | Carbohydrates: 28g | Protein: 3g | Fat: 10g | Saturated Fat: 8g | Cholesterol: 13mg | Sodium: 291mg | Potassium: 160mg | Fiber: 2g | Sugar: 12g | Vitamin A: 845IU | Vitamin C: 0.9mg | Calcium: 29mg | Iron: 1mg
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    About Kristen Chidsey

    Hi, I am Kristen, creator of A Mind "Full" Mom. I believe that making a wholesome family meal does not need to be hard or expensive! I love nothing more than to share with you delicious solutions for your hungry family.

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    1. Mm

      January 15, 2023 at 6:54 pm

      5 stars
      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.

      Reply
    2. E

      January 01, 2022 at 9:52 am

      4 stars
      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?

      Reply
      • Kristen Chidsey

        January 01, 2022 at 2:42 pm

        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.

        Reply
    3. Rachel

      November 17, 2021 at 1:29 pm

      5 stars
      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.

      Reply
      • Kristen Chidsey

        November 17, 2021 at 2:28 pm

        Thanks so much for sharing your review AND your tips Rachel!

        Reply
    4. Michelle

      March 02, 2021 at 11:06 am

      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!

      Reply
      • Kristen Chidsey

        March 02, 2021 at 11:13 am

        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.

        Reply
    5. Emily

      November 15, 2020 at 2:38 pm

      Hi Kristen,

      Would coconut butter work in lieu of coconut oil?

      Emily

      Reply
      • Kristen Chidsey

        November 15, 2020 at 6:35 pm

        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.

        Reply
        • Emily

          November 15, 2020 at 10:17 pm

          Thank you!

          Reply
    6. Maryanne

      November 02, 2020 at 6:48 am

      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.

      Reply
      • Kristen Chidsey

        November 02, 2020 at 6:52 am

        I am so glad these turned out despite the missing egg--that is a great thing for those with egg allergies to know 🙂

        Reply
    7. Alina Moro

      October 05, 2020 at 11:32 am

      Have you tried to make it gluten free?

      Reply
      • Kristen Chidsey

        October 05, 2020 at 1:23 pm

        I have made these with Bob's Red Mill 1:1 Gluten-Free Flour with success.

        Reply
    8. Beth

      September 24, 2020 at 4:53 pm

      5 stars
      These are the perfect Fall treat!

      Reply
    9. Nellie Tracy

      September 24, 2020 at 4:47 pm

      5 stars
      Delicious recipe! Love making this recipe for breakfasts!

      Reply
    10. Joanne

      January 11, 2020 at 4:42 pm

      3 stars
      These were definitely moist but rather tasteless. Could double the spices and use chocolate chips. Will try again.

      Reply
      • Kristen Chidsey

        January 11, 2020 at 6:16 pm

        I am sorry you found these not flavorful enough for your tastes. My son does love these with chocolate chips.

        Reply
    « Older Comments

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    These are the BEST healthy pumpkin muffins out there! Even though this recipe uses all whole wheat flour, maple syrup, and is dairy-free, these pumpkin muffins are light, moist, tender, and perfectly spiced. They are the best from-scratch EASY muffin recipe to satisfy that pumpkin spice craving!

    Meet a Mind "Full" Mom

    A Picture of A Mind"Full"Mom

    Hi! I'm Kristen. I want to welcome you into my kitchen and my REAL, imperfect life. Let me share with you tips and tricks to help you make healthy eating a reality for your family in the chaos of life and on the constraints of a budget. Read more

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    These are the BEST healthy pumpkin muffins out there! Even though this recipe uses all whole wheat flour, maple syrup, and is dairy-free, these pumpkin muffins are light, moist, tender, and perfectly spiced. They are the best from-scratch EASY muffin recipe to satisfy that pumpkin spice craving!

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