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Home » Recipes » Breakfast & Brunch

Healthy Pumpkin Muffins

By: Kathryn Doherty | Last Updated: Mar 10, 2025 | Published: Jun 6, 2015
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These 1-bowl healthy pumpkin muffins are moist and delicious! They are naturally sweetened, 100% whole wheat and perfect for a healthy fall breakfast or snack!

Whole wheat pumpkin muffins in their wrappers and arranged on a white plate.


 

My kids have been eating these since I don’t know when.

Well, let's see. You can’t give honey to a baby before age 1 — nor would I dream of letting an infant have honey or sugar — but I let M have sweetened things starting around 18 months. J a little earlier. Second baby 😉 So that's when.

Still, it feels like I’ve been making batches of these for ages and ages. It’s one of their very favorites and I know why.

Close up of a pumpkin muffin in a muffin liner.

These are loaded with pumpkin and lovely spices and have a wonderful moistness to them. The oil makes them nice and hearty, too, and I feel good about giving them some healthy fats.

And they make your house smell AMAZING!Another great fall muffin recipe you might want to check out is these apple cider muffins that are also whole grain and naturally sweetened.

Recipe Notes:

  • Flour: I use white whole wheat flour, which is 100% whole grain but has a lighter consistency and taste. You can also use whole wheat flour, all-purpose flour, or use a mixture of all-purpose and whole wheat flour if you prefer.
  • Oil: I use canola oil for these muffins. You could substitute vegetable oil or coconut oil if you prefer.
  • Lightened up: If you want a lighter version for adults, you can sub part or all of the oil with unsweetened applesauce.
  • Bread: If you want to bake this as pumpkin bread, instead of muffins, just pour the batter into a greased 9x5 bread pan and bake for 30-40 minutes, until a toothpick inserted in the middle comes out clean.
  • Nuts: You can add ½ cup chopped walnuts or pecans to the batter if you'd like.
A white plate of healthy pumpkin muffins with a text overlay on the photo.

Pumpkin is a year-round thing in our house, not at all reserved for autumn. See pumpkin chocolate chip oat bars. A fave!

And these whole wheat pumpkin muffins are one of our “restaurant/weekend” lunches for the kids. We know it will make them happy and eating, so we can enjoy our food, too.  Beet hummus does the trick, as well.

I've also got a peanut butter pumpkin muffin recipe, with optional chocolate chips, for a different twist!And my healthy pumpkin bread is a fall favorite of the kids and adults. It's so light and springy!

An unwrapped pumpkin muffin on a counter beside a plate full of muffins.

I love muffins, though, for how portable they are. And they also freeze great.

Storage Tips:

  • Pumpkin muffins, once cooled, can be stored in a covered container at room temperature for up to 3-4 days.
  • You can also store them in the refrigerator to extend the shelf life. They'll keep for 5-6 days.
  • They freeze beautifully too! Let the muffins cool completely then wrap each one in aluminum foil. Place the wrapped muffins in a freezer-safe ziplock bag. Label and date it and freeze the muffins for up to 5-6 months. Let thaw overnight in the refrigerator or unwrap and pop in the microwave, directly from the freezer, to reheat.

It's so helpful to have healthy, homemade food like this on hand to make breakfast, school lunch packing and after school snacking that much easier.

Hope you get as addicted to these as we are!

Enjoy!

XO,Kathryn

Eight healthy pumpkin muffins arranged in a circle on a white plate.
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4.13 from 91 votes

Healthy Pumpkin Muffins

These 1-bowl healthy pumpkin muffins are moist and delicious! They are naturally sweetened, 100% whole wheat and perfect for a healthy fall breakfast or snack!
Prep Time10 minutes mins
Cook Time20 minutes mins
Total Time30 minutes mins
Yield: 12 muffins

Ingredients

  • 1 ½ cups white whole wheat flour (see notes)
  • 1 ½ teaspoons cinnamon
  • 1 teaspoon ground ginger
  • ½ teaspoon nutmeg
  • ⅛ teaspoon cloves
  • 1 teaspoon baking soda
  • ¼ teaspoon baking powder
  • ½ teaspoon salt
  • 2 large eggs
  • ½ cup oil (see notes)
  • ½ cup honey
  • 1 teaspoon pure vanilla extract
  • 1 heaping cup pumpkin puree

Instructions

  • Preheat oven to 350.
  • In a large bowl, combine the dry ingredients - the flour through the salt.
  • Make a well in the center and add the eggs, oil, honey, vanilla and pumpkin. Stir wet mix together in the well and then stir together with the dry ingredients until combined. Don't overmix.
  • Line a muffin tin with muffin liners and distribute the batter evenly. They will be about ⅔ full.
  • Bake for 18-22 minutes, until a toothpick comes out clean.
  • Let cool and store at room temperature for 3-4 days or wrap in aluminum foil and store in the freezer for up to 3 months.

Notes

Flour: I use white whole wheat flour, which is 100% whole grain but has a lighter consistency and taste. You can also use whole wheat flour, all-purpose flour, or use a mixture of all-purpose and whole wheat flour if you prefer.
Oil: You can sub applesauce for part or all of the oil if you want to cut some calories. I used canola oil but you can use coconut oil if you prefer.
Nuts: You can add ½ cup chopped walnuts or pecans to the batter if you'd like.
Bread: If you want to bake this as pumpkin bread, instead of muffins, just pour the batter into a greased 9x5 bread pan and bake for 30-40 minutes, until a toothpick inserted in the middle comes out clean.
Storing: Store the muffins, once cooled, in a covered container at room temperature for up to 3-4 days. Or store in the refrigerator for up to 5-6 days.
Freezing: Once cooled, wrap individual muffins in a strip of aluminum foil. Place the wrapped muffins in a freezer-safe ziplock bag, that has been labelled and dated, and freeze for up to 5-6 months.

Nutrition

Serving: 1serving | Calories: 198kcal | Carbohydrates: 25g | Protein: 3g | Fat: 11g | Saturated Fat: 1g | Polyunsaturated Fat: 9g | Cholesterol: 31mg | Sodium: 217mg | Fiber: 2g | Sugar: 12g
Tried this recipe?Leave a comment below or follow me on Instagram @familyfoodonthetable and tag me in your photo!
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Reader Interactions

Comments

  1. Malinda @mybrownpaperpackages

    September 24, 2015 at 7:00 am

    I love baking with pumpkin and I know my kids will eat these so I'm adding it to my Pinterest arsenal. And yes, the second child gets the softer parenting 🙂

    Reply
    • Kathryn

      September 24, 2015 at 6:55 pm

      Thanks Malinda! My kids are addicted to these. They are a must-have around here 🙂 And glad to know I'm not the only one slacking a bit on the second child 😉

      Reply
  2. Sammie @ The Annoyed Thyroid

    September 24, 2015 at 7:54 am

    I love baking with pumpkin and that spice combo is just the best!

    Reply
    • Kathryn

      September 24, 2015 at 6:56 pm

      Thanks Sammie! These seriously smell amazing when they are baking and fresh from the oven! So warm, so comforting, so delicious!

      Reply
  3. Lucy @ Bake Play Smile

    September 24, 2015 at 5:49 pm

    How yummy!!! I love that these are a bit healthy too. Perfect for a mid morning treat. Thanks for linking up with our Fabulous Foodie Fridays party xx

    Reply
    • Kathryn

      September 24, 2015 at 6:56 pm

      Thanks for hosting, Lucy! These are definitely a good morning snack... and breakfast... and afternoon snack... and midnight snack... 🙂 XO

      Reply
  4. Jenny Rice

    November 12, 2016 at 3:40 pm

    I've made these three times already this fall. What a great use for our cooked up jack o lantern! Since I'm almost incapable of following a recipe, I did sub ALL the oil for applesauce. I also add raisins and pecans. They are amazing! Perfect for a mid morning snack, or even part of breakfast for the kids. Thanks!!

    Reply
    • Kathryn

      November 12, 2016 at 6:53 pm

      That's so great Jenny! We eat these on repeat ALL year long! So much for being seasonal... 😉 Love your substitutions/additions - will have to do that to mix things up!

      Reply
  5. Linda George

    July 16, 2017 at 2:43 pm

    My husband and I are trying to cut down on sugar. I love this recipe except for the honey. Is there a substitute for it? Thanks! Just found your site today and love it!

    Reply
    • Kathryn

      July 16, 2017 at 8:54 pm

      Hi Linda! Most baked goods needs some sort of sweetener. I use honey for these since it's a natural sweetener. You could try substituting maple syrup or reducing the amount of honey a bit if you are OK with less sweet things. You could also try substituting mashed banana or unsweetened applesauce but I haven't tried that and can't vouch for the results. I hope that helps and would love to hear what you think!

      Reply
    • Heather

      July 08, 2019 at 12:57 am

      Hey Linda! I have been researching the science of baking. For 1 C of whole wheat flour you need 3-4 Tbsp. of sweetener. So for the 1.5 C of whole wheat flour this recipe calls for, you should probably plan on 1/3 C of sweetener, but I wouldn't go any lower. The type of sweetener is totally up to you, and different ones will obviously change the end flavor some. Good luck!!!

      Reply
  6. Jenni

    February 15, 2019 at 9:51 pm

    I’ve made these several times, starting with Thanksgiving breakfast, and they are a big hit. I’ve made a batch with chocolate chips mixed in, a batch with pecans, and tonight my son suggested mixing both in. I used all applesauce and no oil to make up for the chocolate chips and pecans. I also have used maple syrup in place of the honey as I love the flavor of maple with pumpkin.

    Reply
    • Kathryn

      February 18, 2019 at 3:10 pm

      I'm so happy to hear you love these muffins Jenni! And thanks for sharing your additions and substitutions - that's really helpful! (And also sounds yummy!)

      Reply
  7. Lisa

    August 17, 2019 at 5:09 pm

    Can I sub Greek yogurt for oil?

    Reply
    • Jenni

      August 17, 2019 at 5:36 pm

      I usually sub applesauce for it, and it comes out great. Greek yogurt should work well, too.

      Reply
    • Kathryn Doherty

      August 18, 2019 at 3:51 pm

      Agree with Jenni! You can use applesauce in place of the oil, which works well consistency wise. Greek yogurt is a lot thicker so you probably wouldn't use as much but you could try it that way too.

      Reply
  8. Afton

    March 09, 2020 at 1:34 pm

    Hey! My daughter has Celiac disease, can i sub GF flour for the whole wheat flour in this recipe? Any other adjustments I would have to make? Thanks!

    Reply
    • Kathryn Doherty

      March 09, 2020 at 2:55 pm

      Hi Afton! Yes, you can substitute a gluten-free baking mix for the whole wheat flour in this recipe. The muffins likely won't rise much, but hopefully the flavor will still be great. Would love to hear if you try it!

      Reply
  9. rotisserie

    December 28, 2020 at 6:25 am

    good work.

    Reply
  10. Delie

    January 30, 2022 at 2:49 pm

    These were delicious! I wanted to make pumpkin cream cheese muffins, so I put about 3/4 of the batter into the muffin tin, added a spoonful of neufchatel cheese to each muffin, and topped with the remaining batter. They needed a couple of extra minutes in the oven but turned out beautifully. I also reduced the honey to a generous 1/4 cup and added stevia.

    Reply
    • Kathryn Doherty

      February 01, 2022 at 7:31 am

      I'm so happy to hear you enjoyed them! And love those tweaks you made - sounds delicious! Thanks for sharing!

      Reply
4.13 from 91 votes (91 ratings without comment)

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Hi there! I’m Kathryn Doherty, a cookbook author, mom of two, and devoted food and home cooking nut. I’ve got lots of easy recipes to help you get delicious food on the table for your family!

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