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Home Recipes By Meal Dessert

The Best Healthy Pumpkin Muffins

121 Reviews Recipe
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By: Erin Antoniak • Updated On May 23, 2026

This post may contain affiliate links. Please read my disclosure policy.

A cross between a dessert and a nutritious breakfast, these healthy pumpkin muffins are completely gluten-free! The fresh pumpkin puree and chocolate chips elevate these muffins to icon status.

bite into pumpkin muffin

Sweet healthy pumpkin muffins

These healthy pumpkin muffins are the perfect things to make for a fall snack, portable breakfast, or autumn brunch. They are sweet while not wreaking havoc on your blood sugar.

These muffins are never going to let you down. I mean, you will know they are going to be perfect right away because the pumpkin batter is fluffy and thick. You can tell that when you are pouring them into your muffin tin, these will be the softest pumpkin muffins you have ever had!

I think these pumpkin muffins rival the ones from Dunkin’ – while being better for you at the same time. These are perfectly soft, full of pumpkin spice, fluffy, and just so freaking good that you will want to eat them for breakfast every single day.

overhead best healthy pumpkin muffin in tray

Ingredients in these pumpkin oat muffins

The ingredients in these muffins are the best because they are simple and most likely ones that you already have on hand in your pantry. Baking can be really easy if you allow it to be!

I love to use recipes that don’t require fancy ingredients or anything that you wouldn’t already have at home. All you really need for these muffins:

  • Oat Flour– Oats are a heart-healthy whole grain. You’ll need 2 cups of oat flour.
  • Pumpkin Puree – Either use fresh pumpkin puree from your Jack-O-Lantern or add some from a can, but either way, use 1 cup.
  • Maple Syrup – Sweeten the muffins naturally with 1/3 a cup of real maple syrup.
  • Eggs – These are an emulsifier, so you’ll use 2 large eggs.
  • Coconut Oil – or Other Oil of Choice – Melt 1/2 a cup of your favorite type of healthy oil.
  • Baking Soda + Powder – Combine 1 teaspoon of baking powder with 1/2 a teaspoon of baking soda for the fluffiest muffins.
  • Vanilla – Pure vanilla extract adds deeper and richer flavors to the muffins, use one teaspoon.
  • Pumpkin Pie Spice – Use some premade pumpkin pie spice to really make them taste amazing – about two teaspoons.
  • Chocolate Chips – These chocolate chips are optional. If you want to use them, add about one cup.
the best healthy pumpkin muffins

Kitchen tools required

You don’t need any fancy kitchen gadgets to make this simple pumpkin muffin recipe. Grab the following tools before you begin.

  • Muffin Tin
  • Muffin Liners
  • Large Bowl
  • Whisk
  • Small Bowl
  • Wooden Spoon

For measuring, you will need 1 cup, 1/2 cup, 1/3 cup, 1 teaspoon, and 1/2 teaspoon.

half of pumpkin muffin

How to make the best pumpkin muffins

These best-ever healthy pumpkin muffins are so easy to make. You’ll want to start by making homemade oat flour which is way easier than it sounds. No fancy mills or grinding machines here, all you need is a blender!

Just throw some oats into a blender and pulse for 10 seconds or so until your oats are finely ground into flour.

Tip: Always measure the amount of oats you need after grinding your oats up because the measurement can change.

If you already have oat flour, you can skip this step and move directly to mixing the pumpkin muffin batter.

Put the oat flour aside and whisk together your eggs, oil, pumpkin, maple syrup, and vanilla until well combined.

Mix the oat flour, baking powder, baking soda, salt, and cinnamon in another bowl.

Add the dry ingredients into the wet ingredients and stir until completely combined. Then add in any mix-ins you want! I love adding chocolate chips or pecans to my pumpkin muffins. I even save some to put on top!

Pour batter into a lined and greased muffin tin, top with a little extra chocolate and crushed nuts if desired, and bake! Bake them until you insert a toothpick into the middle, and it comes out clean.

half of pumpkin muffin

Recipe Tips

Here are some questions people often ask about making pumpkin muffins. If you don’t see your question in this list, please leave it in the comments.

What other ingredients can I add to these oat flour pumpkin muffins?

You could add some cocoa powder to the muffins to make chocolate pumpkin muffins. Instead of chocolate chips, use white chocolate chips.

Should I make my own homemade oat powder?

This is entirely up to you. Some people like to make their own oat powder by pureeing rolled oats because it is less processed. It could be cheaper to make your own oat powder, especially if you buy rolled oats in bulk.

Can I turn this into a loaf of quick bread?

Yes, you can easily place the batter into a prepared loaf pan and make healthy pumpkin bread. You will have to adjust the baking time because it will take longer for the bread to bake.

Are these pumpkin muffins keto-friendly?

No, these muffins are not good to eat on a low-carb diet. The oat flour makes them much too high in carbs. Plus, the maple syrup increase that number even more. I suggest looking for a muffin recipe that uses either almond flour or coconut flour and is sweetened with a sugar substitute.

Storing leftovers

Storing muffins is simple. We like to let our muffins sit at room temperature in a sealed Tupperware container for up to four days. After that, we will do one of two things to ensure that they are stored properly – store them in the freezer or the refrigerator.

Freeze the muffins

Once cooled, wrap them up individually in plastic wrap and place them in a gallon Ziploc bag. This makes it easier to pull them out individually. Store them in the freezer for up to 6 months. When you are ready to eat them again, just let them thaw naturally in the refrigerator overnight.

Refrigerate them

This will increase the shelf life to longer than four days. Just stick the sealed, airtight container right into your fridge, and you will be good to go! These muffins will last about a week in the refrigerator.

If you liked this recipe, you’ll want to try these!

  • Paleo Banana Bread Muffins
  • Chocolate Zucchini Muffins
  • Paleo Pumpkin Bread

If you make this recipe, be sure to comment below and let me know how it was! Also tag @erinliveswhole on Instagram and use the hashtag #erinliveswhole so I can see it and feature you!

healthy pumpkin muffins

If you tried this recipe or any other recipes on my blog, please leave a 🌟 star rating and let me know how it went in the 📝 comments below. Follow @erinliveswhole on Instagram and tag me in any of the recipes you make so I can repost them!

over head pumpkni muffins
5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.9 from 121 reviews

The Best Healthy Pumpkin Muffins

Healthy pumpkin muffins are easy to make and made totally gluten free with certified gluten free oatmeal, fresh pumpkin puree, and a handful of chocolate chips! Toddlers, kids, teenagers, and adults all love these for a simple snack!

Prep: 10 Cook: 20 Total: 30 minutes
Yield 12 muffins 1x
Scale
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Ingredients

  • 1 cup pumpkin puree
  • 1/2 cup coconut oil, melted
  • 2 eggs
  • 1/3 cup maple syrup
  • 1 tsp vanilla
  • 2 cups oat flour , loosely scooped, not packed. gluten-free if necessary. see notes for homemade.
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 2 tsp pumpkin pie spice
  • Optional: chocolate chips /chopped pecans – about 1 cup.

Instructions

  1. Preheat oven to 350F and line a muffin tin with liners and nonstick spray.
  2. In a large bowl, whisk pumpkin, coconut oil, eggs, maple syrup, and vanilla until well combined.
  3. In a small bowl, mix oat flour, baking powder, baking soda, salt and pumpkin pie spice.
  4. Add dry ingredients to wet and stir until combined. Stir in any mix-ins.
  5. Scoop into muffin tin and bake for about 22 minutes or until toothpick inserted comes out clean.
  6. Enjoy!

Notes

Make homemade oat flour by grinding oatmeal until very fine in a blender, measuring after blended.

Author: Erin Antoniak Category: breakfast, gluten-free Method: oven
over head pumpkni muffins

Did you make this?

Leave a comment below and tag @erinliveswhole on social media!

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There may be affiliate links in this post! By purchasing a product I recommend, I may receive a small compensation. However, I only recommend products I absolutely love and use myself. Thank you for supporting Erin Lives Whole, it helps keep this blog afloat 🙂

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Recipe Rating




  1. Erin says

    Posted on 10/17 at 9:03 am

    Loved these muffins Erin! But mine crumbled a ton when I took them out of the oven. I did store the batter in the fridge for about 30 minutes prior to baking, could this have caused the issue ?? I am going to re attempt this weekend I think ! I am also baking in Colorado ( higher altitude ) so not sure if this played a part as well

    Reply
    • Erin says

      Posted on 10/18 at 7:06 pm

      Hi Erin, so happy you love them!! Oat flour gets really dry really fast, so I suggest baking right away. Also may need to add a little more oil next time! Let me know how that comes out for you!

      Reply
  2. Debra says

    Posted on 10/14 at 4:38 pm

    I love using oatmeal flour. I added lemon zest and 1 TBS of lemon juice, and used 1 1/2 cups roasted butternut squash. Delicious!

    Reply
    • Erin says

      Posted on 10/16 at 1:07 pm

      Hi Debra, so happy you loved them and made them your own!!

      Reply
  3. Amy says

    Posted on 10/13 at 6:47 pm

    Just delicious! Big wow from my family. Perfectly light and the right amount of sweetness. My new go-to.

    Reply
    • Erin says

      Posted on 10/16 at 1:05 pm

      Hi Amy, so happy you loved them so much! 🙂

      Reply
  4. Dale says

    Posted on 10/9 at 6:30 pm

    These muffins are the perfect pumpkin bite. Delicious is an understatement! Will be in my regular fall recipe rotation. They disappeared!

    Reply
    • Erin says

      Posted on 10/10 at 8:23 pm

      Hi Dale, so glad you loved them!! 🙂

      Reply
  5. Kathleen says

    Posted on 10/9 at 4:17 pm

    I made your healthy pumpkin muffins and they are so yummy. Thanks for the delicious foods you share with us.

    Reply
    • Erin says

      Posted on 10/10 at 8:22 pm

      Hi Kathleen, so glad you loved them!! 🙂

      Reply
  6. Theresa says

    Posted on 10/4 at 8:53 pm

    Can you use quick oats/min oats?

    Reply
    • Erin says

      Posted on 10/5 at 3:41 pm

      Hi Theresa, yep that should be fine. Let me know how they come out!

      Reply
  7. Hannah W. says

    Posted on 10/4 at 7:53 pm

    Erin killed it again!! This recipe was so intimidating after seeing “oat flour” but knew Erin wouldn’t have posted if she wasn’t in love. So glad I can eat these with slightly less guilt because it’s a 2 or 3 serving kind of muffin!

    Reply
    • Erin says

      Posted on 10/5 at 3:40 pm

      Hi Hannah, so happy you loved the muffins! 🙂

      Reply
  8. Alyssa says

    Posted on 10/2 at 7:33 pm

    Moist, flavorful, and clean ingredients. Yay! I was expecting the homemade oat flour to leave these claggy and pasty, but nope! I will experiment with the amount of oil in the future, but am very pleased with these!

    Reply
    • Erin says

      Posted on 10/4 at 1:42 pm

      Hi Alyssa, so happy you loved them!

      Reply
  9. Cynthia Solis says

    Posted on 9/25 at 6:43 pm

    I love the idea of this healthy muffins
    ! Unfortunately I used organic agave instead of maple syrup and it wasn’t sweet enough : (
    Just sharing in case anybody thinks about doing that.
    Also, mine were a little dry . Any idea why that could be? I didn’t change anything else in the recepy.
    Thank you !!

    Reply
  10. Peggy says

    Posted on 9/15 at 3:33 pm

    i only have almond flour in the kitchen today
    is it ok to substitute it for the oak flour
    in the pumpkin muffin recipe
    thank you
    Peggy

    Reply
    • Erin says

      Posted on 9/16 at 11:03 am

      Hi Peggy, I haven’t tested with that specific flour, and most gf flours work on a totally different absorption rate. You can definitely give it a try but you’d likely have to adjust the amount. Let us know if it works!

      Reply
  11. Belle says

    Posted on 9/13 at 12:26 pm

    Just made these last night! They turned out great! The only thing is when I put my batter into the liners, I thought it would spread out while it baked. It didn’t and just retained its shape. I thought it was going to be dry because of that but when I took a bite, it was so soft and fluffy! Did not expect that from the look of it. Any idea why my batter didn’t spread while baking? Thanks so much!

    Reply
  12. Melissa says

    Posted on 9/5 at 5:00 pm

    Do you think butter would work instead of coconut oil? Or even half butter half coconut oil? Thanks! 🙂

    Reply
    • Erin says

      Posted on 9/12 at 4:07 pm

      Hi Melissa, yes- perfectly! Let me know how they come out!

      Reply
  13. Cheryl says

    Posted on 4/27 at 12:21 pm

    These are so amazing… when I clicked the 2x to double it didn’t double the amount of chocolate chips so that was a fail on my part cause those chocolate chips were definitely missed. These will be on repeat for sure.

    Reply
    • Erin says

      Posted on 4/27 at 3:49 pm

      Hi Cheryl, so glad you loved them and oh no! They don’t double when you double the recipe since they are optional but so glad you still enjoyed the muffins!!

      Reply
  14. Kim says

    Posted on 4/19 at 3:47 pm

    These are SO GOOD. I’m making them for the second time this week 🙂 They’re so pumpkin-y and I love that they aren’t too sweet. They go perfectly with coffee or for dessert. Thanks!!

    Reply
    • Erin says

      Posted on 4/20 at 2:37 pm

      Hi Kim, so happy you loved the muffins!!

      Reply
  15. Kylie says

    Posted on 3/2 at 3:01 pm

    Can I sub oat flour for gluten free flour?

    Reply
    • Erin says

      Posted on 3/3 at 11:40 am

      Hi Kylie, I haven’t tried it but that should be ok. Just triple check the ratio since now all flours are 1:1 and let me know how they come out!

      Reply
      • Donna says

        Posted on 3/21 at 12:32 am

        Could I use almond flour or a coconut flour or cassava flour instead of the oats flour since I am allergic to it?

      • Erin says

        Posted on 3/21 at 5:18 pm

        Hi Donna, that should work! Just double check the flour ratio since not all are 1:1. Let me know how your muffins come out!

  16. Kim says

    Posted on 3/1 at 1:27 pm

    Oh my goodness! Hands down the best muffin recipe! I used half coconut oil/half applesauce. Halved the recipe so it only made 6 muffins (just in case they didn’t turn out for me)…may have eaten 4 😉. These go in the dangerous category. Next time, I’ll be doubling the recipe! Thank you for the yumminess!

    Reply
    • Erin says

      Posted on 3/1 at 3:38 pm

      Hi Kim, so happy you loved them! 🙂

      Reply
  17. Jocelyn says

    Posted on 12/28 at 4:56 pm

    BEST RECIPE EVER!!! I think they taste better every time I make them 🙂

    Reply
    • Erin says

      Posted on 12/28 at 5:49 pm

      Hi Jocelyn, so glad you loved them!!

      Reply
  18. Alicia says

    Posted on 11/26 at 6:07 pm

    I’ve made this recipe many times and it’s always a hit! Today, my 8 year old helped me and he had a blast. I love that they’re naturally sweetened and use oat flour. Delicious!

    Reply
    • Erin says

      Posted on 11/28 at 1:49 pm

      Hi Alicia, I am so glad everyone loves them and that he helps you! How fun!!

      Reply
  19. Victoria says

    Posted on 11/16 at 10:08 am

    I´m making these in my PHS class. It is a big grade and I hope it goes well.

    Reply
  20. Michele says

    Posted on 11/5 at 10:27 am

    Im not a baker, to many things have gone wrong! BUT, I want to make these muffins for my son. What can I substitute for the eggs?

    Reply
    • Erin says

      Posted on 11/5 at 12:59 pm

      Hi Michele, you could use applesauce or a flax egg. Let me know how the muffins come out!

      Reply
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I’m Erin. Creator of Erin Lives Whole, a food blog with delicious and easy healthy recipes that will leave you feeling good. We’ve got everything from wholesome baked goods to comforting savory dishes. I can’t wait to see what you whip up! Read More...

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