Healthy Pumpkin Muffins

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Healthy Pumpkin Muffins are made with whole wheat flour, Warm spices, pumpkin, coconut oil, and sweetened with pure maple syrup. These easy and delicious muffins make a great fall breakfast or snack!

Pumpkin Muffins

Pumpkin Recipes

I love baking with pumpkin and make quite a few decadent pumpkin recipes. For example, have you tried my Pumpkin Chocolate Chip Cookies, Pumpkin Sheet Cake, or Pumpkin Bundt Cake? They are all SO good and worth every single bite, but I thought it was time I made a healthy pumpkin recipe. Let me introduce you to my Healthy Pumpkin Muffins. They are on the healthier side, but you will never know it because they are super delicious. So delicious that my boys called them pumpkin cupcakes at first…ha! I fooled them:)

Healthy Pumpkin Muffins

How to Make Healthy Pumpkin Muffins

I promise this muffin recipe is super simple and you won’t even know they are on the healthy side because they are SO delicious! To make healthy pumpkin muffins, you need a few key ingredients:

  • White whole wheat flour or whole wheat flour. I like to use white whole wheat flour because it is lighter in color and texture. My boys don’t even know they are eating whole wheat muffins. Regular whole wheat flour will work well too. If you want to make gluten-free pumpkin muffins, you can use all-purpose gluten-free flour, I like Cup4Cup or Bob’s Red Mill.
  • Pumpkin. This one is obvious, but make sure you use pure pumpkin puree and not pumpkin pie filling. The pumpkin is a healthy addition to the muffins and keeps the muffins super moist without adding any fat or sugar.
  • Coconut oil. Instead of using butter, I use melted coconut oil.
  • Pure maple syrup. The muffins are sweetened with pure maple syrup, there are no refined sugars in this pumpkin muffin recipe. Make sure you buy PURE maple syrup, you want the good stuff! The maple flavor is so good and adds the perfect amount of sweetness.
  • Almond milk. I use unsweetened vanilla almond milk in this recipe because there are no added sugars. You can use regular milk or buttermilk if you wish.
  • Eggs. You will need two large eggs to make the muffins. I love the protein they add. If you need the recipe to be vegan, you can use a flax eggs.
  • Spices. Adding in ground cinnamon, ginger, nutmeg, and cloves gives the muffins a ton of flavor! The warm fall spices compliment the pumpkin perfectly!

Muffin Tips

I love this pumpkin muffin recipe because they are so easy to make. You don’t even need a mixer. There are a few key tips I want to share for baking muffins.

  • Make sure you line the muffin pan with paper liners or grease the muffin cups with nonstick cooking spray.
  • Measure all of your dry ingredients and put them in a bowl. Use a whisk to combine them all together.
  • Make sure all of your wet ingredients are at room temperature.
  • When you combine the dry ingredients and the wet ingredients, don’t over mix the batter. If you do, you will have dense, tough muffins and they won’t rise as much.
  • Fill the muffin cups about ¾ of the way full.
  • I like to sprinkle the muffins with turbinado sugar before they go in the oven. The sparkly, sugary crunch is always a nice finishing touch!
  • Don’t over bake the muffins. Take them out with a toothpick inserted into the center comes out clean.
  • Let the muffins cool before eating.

Mix it Up

I love a plain pumpkin muffin, but if you want to mix things up you can add the following ingredients.

  • 1 cup dark chocolate chips or mini chocolate chips. Yes, they are healthy pumpkin muffins, but I won’t tell if you add chocolate. Chocolate is always a good idea and SO good for mental health:)
  • 1 cup dried cranberries or raisins
  • 1 cup chopped walnuts or pecans
  • You can also top the muffins with pepitas or old-fashioned oats.
  • If you are feeling fancy, you can glaze the muffins with a maple or orange glaze.

Can You Freeze Pumpkin Muffins?

YES! I love making these muffins because they do freeze well. Let the muffins cool completely and then put them in a freezer bag or freezer container and freeze for up to 2 months. When ready to eat, you can let them defrost on the counter or you can pop them into the microwave for about 30 seconds. I love having a stash in the freezer for busy mornings. The boys love grabbing one before school.

Perfect for Breakfast or Snack Time

Are you ready to bake some pumpkin muffins? I sure hope so! These healthy muffins make a great breakfast. You can make them on a lazy weekend morning or you can whip up a batch during the week so you can grab a muffin and go! There is no wrong morning to make and enjoy pumpkin muffins. They also make a great fall snack. Enjoy with a glass of milk and you are all set!

If like these pumpkin muffins, you might also like:

Pumpkin Muffins Recipe

Healthy Pumpkin Muffins

These easy pumpkin muffins are a fall favorite for breakfast or snack time. You will never know they are healthy because they are SO delicious!
4.69 from 92 votes


  • 1 3/4 cups white whole wheat flour or whole wheat flour
  • 1 teaspoon baking soda
  • 1 1/2 teaspoons ground cinnamon
  • 1/2 teaspoon kosher salt
  • 1/2 teaspoon ground ginger
  • 1/4 teaspoon ground nutmeg
  • 1/8 teaspoon ground cloves
  • 1 cup pumpkin
  • 2 large eggs at room temperature
  • 1/2 cup pure maple syrup
  • 1/3 cup coconut oil melted and cooled to room temperature
  • 1/4 cup unsweetened vanilla almond milk at room temperature (or milk of your choice)
  • 1 1/2 teaspoons pure vanilla extract
  • Turbinado sugar for sprinkling on muffins, optional


  • Preheat oven to 350 degrees F. Line a 12-cup muffin pan with paper liners or grease the cups with nonstick cooking spray. Set aside.
  • In a medium bowl, whisk together the flour, baking soda, cinnamon, salt, ginger, nutmeg, and cloves. Set aside.
  • In a large bowl, combine the pumpkin, eggs, maple syrup, cooled coconut oil, milk, and vanilla extract. Stir until smooth.
  • Add the dry ingredients to the wet ingredients and stir with a spatula until just combined. Don't over mix.
  • Pour the muffin batter evenly into the prepared muffin cups. Sprinkle the muffins with turbinado sugar, if using. Bake for 20-24 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Let the muffins cool and enjoy!


Calories: 163kcal, Carbohydrates: 22g, Protein: 3g, Fat: 7g, Saturated Fat: 5g, Cholesterol: 27mg, Sodium: 206mg, Potassium: 92mg, Fiber: 1g, Sugar: 8g, Vitamin A: 865IU, Vitamin C: 0.9mg, Calcium: 41mg, Iron: 0.6mg
Keywords healthy pumpkin muffins, pumpkin muffins

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I'm Maria and my husband is Josh. We share a love of cooking, baking, and entertaining. We enjoy creating recipes that are simple, fresh, and family friendly. We love sitting around the table with good food, good conversation, and good friends and family! Our kitchen is always open!
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  1. 5 stars
    Marvellous…! am a big fan of muffins and this pumpkin muffins looks sooo good & more i will definitely make it in upcoming few days….! Thanks for sharing….!

  2. These look delicious. I am wondering if I can substitute light olive oil for the coconut oil? I have read and heard so much lately about how unhealthy coconut oil is…the the initial hype about benefits  has now been disproved. 

  3. I was looking for a recipe like this one!! only problem my son is allergic to egg do you know a substitute for eggs or have you tried without eggs?

    1. In most baked goods you can substitute flaxseed for eggs (called a “flax egg”). 1 Tbsp ground flax seed + 3 Tbsp water, mixed in a bowl and left to sit for 5 minutes is the equivalent of 1 egg.

    1. I am sure a loaf pan would be just fine. Just add baking time, probably 45-60 minutes, depending on your oven.

  4. Hello! Thank you for sharing the recipe. I’m so wondering if I can bake this in a pound cake pan just like your another pumpkin bread recipe. What temperture and how long should I bake it for???

  5. If one cannot have wheat flour can it easily be replaced with coconut flour? Or would the measuring be different?

  6. 5 stars
    I’ve made them twice and we really liked them. I put honey on mine and it was so good.d. It’s a go to recipe for me now. I love using maple syrup in them.

  7. 4 stars
    I liked the recipe but I think 1 teaspoon might be a little too much baking powder – it gives the muffins a metallic after taste.

  8. These sound delicious! I would love to make these!! I would like to get nutritional value—calories, carbs, etc. Thank you!

  9. 5 stars
    These were SO delicious. I recently made them for family that came to visit our sweet little new babe and they all RAVED about them. I love that they’re made with whole-wheat flour and coconut oil as well. They came super moist and just perfect.

  10. Hi, can honey be used as a substitute for the maple syrup? And if so,  should I use the same measurement? Thanks so much!

    1. I’m a little late, but what she means is pumpkin puree which is cooked. You can either buy a can of the puree at the store. Or if you’re using fresh pumpkin, you need to cook it in the oven. (Find something online, cooking times vary based on size and type) but its roughly about 45 mins-60 mins. You take the chunks of cooked and cooled pumpkin, and put it in a blender until it becomes creamy and consistent.

  11. 5 stars
    These muffins are fantastic. I used who wheat flour which makes them a bit more dense and filling. They are a great snack!

  12. These muffins sound delicious, will definitely try them. I just didn’t get the part of the pumpkin. Do you put the pumpkin raw, do you grate it or Fo you cook it first. Sorry never used pumpkin before.

  13. I really like this recipe. I made some changes, which I know is annoying, so I won’t rate your recipe based on that. But I love that you made something that only uses maple syrup for sweetener and the texture is perfect. Though I use sunflower oil. I also increased the sweetness a bit and adjusted the spices. It’s great without vanilla as well! It’s my number one muffin recipe right now! I put a link for it on my website.

  14. Loved these! I made them exactly like the recipe, and added some raisins to the batter before baking. They are absolutely delicious!!

  15. I am super super excited to make these!! This looks awesome and I love all the ingredients you used in this recipe. My friends and family are going to love it. lovely pictures too 😉

  16. Has anyone substituted the whole wheat flour with oat flour and/or protein flour? curious how they would turn out?

    1. I haven’t tried a silicone pan, but if you are doing mini muffins, I would check them at half the time. Enjoy!

  17. I substituted the coconut oil for Avocado oil, added a cup of raisins, turned out perfect.
    Easy to make a double batch and freeze! Excellent recipe!

  18. 5 stars
    I am always looking for the healthy recipes making from natural food. Your tips are really helpful for me. Thank you so much for your sharing.

  19. I just made these and they are delicious! They have a really nice pumpkin flavor and with the wheat flour and pumpkin, you get some good fiber.

  20. Tasty, fluffy and nutritious. They fill me up and leave me satisfied. I went with the walnuts option. Amazing!

  21. 5 stars
    I made a few substitutions: flax eggs instead of eggs and applesauce instead of coconut oil. They turned out great!

  22. 5 stars
    I made these using 1/2 spelt and 1/2 whole wheat flour. Substituted buttermilk for almond milk. Added hemp hearts and Lily’s dark chocolate chips and they were fantastic!!

    1. I don’t recommend almond flour, the texture is very different. You can use all-purpose gluten free flour. I like Cup4Cup.

  23. I’m new here and got this in an email. I’m newly dairy free and am so excited to see that this is dairy free! Thank you so much! I can’t wait to discover more of your recipes… P. S. These will be made today!

  24. 5 stars
    These are sooo good!!! Family approved and so easy to make. I did sit out my eggs (maybe not totally room temperature) and cooled my coconut oil but the coconut oil did harden into chunks when I mixed the ingredients but it didn’t affect the texture or flavor. Getting ready to make another batch! Great recipe!

  25. Made these pumpkin muffins today. Added mini chocolate chips. They are delicious and 100% kid approved in my household. Thank you!!

  26. 5 stars
    For WW purposes, are the values in the nutrition information per serving for ONE muffin? Great recipe, by the way. My 9-year-old who is SUPER picky was proud to show me he ate one. 🙂

  27. 5 stars
    These are absolutely delicious! I also used regular milk and canola oil, because that’s what I had on hand – turned out perfectly. They’re not too sweet either, making them perfect to add a few chocolate chips on the top – yum! Thank you for yet another great recipe!

  28. 5 stars
    These are excellent muffins, I added chocolate chips but kept everything else exactly the same. My picky 5 year old is obsessed with them. Even my picky mother really likes them. They freeze well too!

  29. 5 stars
    These were sooo good! I followed the recipe exactly and they were full of flavor, moist, great texture. My kids really are very picky, and they loved them too! I have tried so many different healthy muffin recipes that were just not good. So happy to have found one my family enjoys!!

  30. Love anything made with pumpkin. Can I use regular oil or how much butter would I use in place of coconut oil? Thanks. PS: Love your website and all the delicious recipes.

    1. You can use regular oil. If you are going to use melted butter, use the same amount as the oil.

  31. Just made these and they were great!! So flavorful and great texture…we did add chocolate chips, which added just a bit more sweetness.

  32. These were a delicious not-to-sweet option for my 11 month old and myself! I opted for gluten free flour due to sensitivity and they were perfect! I’m saving this recipe for future reference. Thank you!

  33. So happy to find muffins with coconut oil, no refined sugar AND no dairy!! These are delicious and perfect for my non-dairy self (and I can feel good about giving them to my daughter too). I’m going to try it with a little more spice next time because I LOVE fall flavors!

  34. 5 stars
    These are easy and delicious! I substituted canola oil for coconut (because we are not a coconut oil family), honey for the maple syrup because I was out of syrup, and regular oat milk because I love oat milk! Oh, and added chocolate chips because duh…. Otherwise, made it exactly as written. We love them because they are not too sweet, and I can feel good about them because they are pretty darn healthy. Win win!!

  35. 5 stars
    These muffins are absolutely delicious! As I struggle to lose weight, I am very aware of my daily calorie count. These muffins fit…as long as I don’t eat all 12. I added dark chocolate chips to mine – only about 1/3 cup as I was trying to keep the calorie count below 200. These are quick, easy and perfect for the season. I have made 2 batches this week (and it’s only Thursday) so that I could share with family. I was even able to stash a few in the freezer – a tactic to prevent me from inhaling every last one! Thank you for a wonderful and fairly healthy recipe.

  36. 5 stars
    Don’t just sit there. Get the ingredients and make these! We added a few mini white chocolate chips on the top. My search for pumpkin muffins is over. Thanks for sharing!! ❤️

  37. 5 stars
    Made these just as the recipe says, and they’re delicious! I love that these are a healthier choice for my family. I made them for my 4-year-old’s class party, and he loved them so much, he said “mommy you should make these for the whole town!” 🙂

  38. 5 stars
    Absolutely delicious! I omitted the cloves because I find them overpowering, and the result was plenty flavorful. Thank you!

  39. Made these muffins with a couple changes and they turned out great! I used roasted and pureed butternut squash because my garden yielded so many this year. No fancy topping sugar available but still very good. Made again with squash but substituted brown sugar for the very expensive real maple syrup and added a little more liquid = perfectly yummy! Thanks for providing such good recipes that can be modified easily to what I have on hand!!

  40. 5 stars
    Fluffy and delicious! ‘Healthy’ muffin recipes usually turn out dense and heavy muffins but not these–they’re bakery soft. Good pumpkin and fall spice flavor without being overpowering. I doubled the recipe & made a few minor tweaks to up the protein and keep saturated fat down and they were still the lightest fluffy healthy muffins I’ve ever made (and I bake muffins a LOT). Note to anyone else doubling, don’t double the salt–you can taste it a hint if you do. Thanks for the great recipe! This will be my go to.

  41. I would caution folks who believe this recipe is ‘healthy’ as it has coconut oil which is high in saturated fat. You are better off using safflower, grapeseed or avocado oil.

  42. 5 stars
    I am obsessed with this recipe! I love pumpkin so much and I’m thrilled to have a healthy version of a pumpkin muffin. It is positively delicious and guilt free.

  43. I made these today because I found like 6 cans of pureed pumpkin while I was going through my pantry cabinets. They are fantastic!

  44. 5 stars
    This is the second time I made these muffins! followed the recipe exactly and added 1/2 cup dark chocolate chips. Delicious! A fall favourite in my house now. Thanks Maria!

  45. 5 stars
    These are perfect for snacks for my toddler! I like finding easy, healthy recipes for her that also taste good, and this met the mark. Not super sweet, but I like that!

  46. 2 stars
    Made these this morning. Followed recipe as listed with no substitutes. Not one of my 5 boys approved. I was so disappointed but understood when I tasted them. Way too bland (plain wheat muffin more or less). Gave them two stars because I could at least eat it with honey or butter.

  47. 5 stars
    These are the best healthy muffins I’ve tried and I’ve been testing a lot of the recipes online. I did add half a mashed banana, used salted butter instead of coconut oil, and used regular flour.

  48. I am in love with these muffins. Best muffins I’ve made. I used 1 cup all-purpose + 1/4 whole wheat + 1/2 spelt and the texture is really nice. I wanted to use the flours I had but will look for the white whole wheat. I added 1/2 cup mini chocolate chips. Thank you. Great recipe.

  49. 5 stars
    These were excellent! I mill my own flour and used soft white wheat berries. I substituted Grandma’s unsulphured molasses (I was out of maple syrup) and added extra ginger and cinnamon as we like a strong spice muffin. These were moist and flavorful. Tasted a bit more like gingerbread than pumpkin but we loved them. Used the suggestion to sprinkle uncooked tops with turbinado sugar and that gave them a nice crunchy texture. Will defined make again.