Healthy Pumpkin Muffins are made without butter, oil or flour! These naturally gluten-free pumpkin muffins are moist, flavorful and perfectly pumpkin spiced.

Healthy pumpkin muffin split open to reveal the soft and moist interior with melting chocolate chips, ready to be eaten.

Healthy Pumpkin Muffins

These nutritious pumpkin muffins are healthier, with less fat, calories, and sugar than traditional ones. We substitute refined flour with blended old-fashioned oats, use honey instead of sugar, and include a high proportion of canned pumpkin, which is rich in vitamins, nutrients, and antioxidants.

The muffins feature dark chocolate, which provides essential fats and antioxidants, making them a fun choice in these muffins.

Combining wet and dry ingredients for the healthy pumpkin muffin recipe, then filling a prepared muffin tin.

Ingredients

  • Canned Pumpkin: Provides moisture and flavor, making up the base of the healthy pumpkin muffins. Use any leftovers in this healthy pumpkin bread.
  • Sweeteners (Honey, Light Brown Sugar): Add sweetness and help make the texture even better.
  • Vanilla Extract & Egg: Enhance flavor and bind the ingredients.
  • Leaveners (Baking Soda, Baking Powder): Help the muffins rise and become fluffy.
  • Spices (Cinnamon, Nutmeg, Pumpkin Pie Spice): Add warmth and depth to the flavor.
  • Oat Flour: Replaces traditional flour, adding a wholesome texture and nutrients.
  • Dark Chocolate Chips: Introduce pockets of rich, melty flavor.
Oat flour being made in a blender.

How To Make Healthy Pumpkin Muffins

  1. Prepare: Preheat oven and grease a muffin pan.
  2. Mix: Combine wet ingredients in a bowl. In another bowl, mix together dry.
  3. Combine & Bake: Mix together wet and dry ingredients, stir in dark chocolate chips, fill muffin cavities, and bake until tops are set.
  4. Cool & Store: Let cool before removing from the pan and store in an airtight container. Best enjoyed within a few days.
Pumpkin healthy muffins split in half to reveal their delicious and moist interior.

Tips For Success

  • Non-stick Muffin Pan: Use a high-quality non-stick pan for easy removal. Here’s my favorite muffin tin.
  • Pumpkin Type: Choose solid-packed, thick pumpkin like Libby’s for best flavor and texture.
  • Sugar Adjustment: Increase sugar to taste, especially if you’re not accustomed to healthier baked goods. You can vary from 2 tablespoons to 1/2 cup based on preference.
  • Precise Measuring: Level off dry ingredients and ensure liquids like pumpkin and honey are fully transferred into the mixing bowl for these healthy pumpkin muffins.

Storage


Leftovers?

Room Temperature: Store muffins in an airtight container. Best within 1-2 days.

Refrigeration: Keep in an airtight container for up to 5 days. Bring to room temp before eating.

Freezing: Freeze in a single layer, then transfer to a bag or container. Freeze up to 3 months. Thaw at room temp or microwave before serving.

More Healthy Pumpkin Recipes

4.82 from 50 votes

Healthy Pumpkin Muffins

Low-calorie, Healthy Pumpkin Muffins are made without butter, oil, or flour! These naturally gluten-free pumpkin muffins are moist, flavorful, and perfectly pumpkin spiced.
Prep Time: 15 minutes
Cook Time: 22 minutes
Total Time: 37 minutes
Servings: 9 muffins

Ingredients 
 

  • 1 cup canned pumpkin (Note 1)
  • 2 tablespoons honey
  • 4 tablespoons light brown sugar (Note 2)
  • 1 teaspoon vanilla extract
  • 1 large egg
  • 1/4 teaspoon salt
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon baking powder
  • 1 teaspoon cinnamon
  • 1/4 teaspoon nutmeg
  • 1 teaspoon pumpkin pie spice
  • 1 cup + 1 tablespoon oat flour (regular oats that have been blended) (Note 3)
  • 1/2 cup dark chocolate chips

Instructions 

  • PREP: Preheat the oven to 350 degrees F. Spray 9 cavities in a muffin pan with nonstick spray; do not use muffin liners with these; they stick to the liners. Press excess liquid out of the pumpkin with paper towels.
  • WET INGREDIENTS: Combine the pumpkin, honey, brown sugar (See Note 2), vanilla, and egg in a bowl. Beat until combined.
  • DRY INGREDIENTS: In another bowl, stir together the salt, baking soda, baking powder, cinnamon, nutmeg, pumpkin pie spice, and oat flour.
  • MIX TO COMBINE: Add the dry to the wet, mixing until just combined. Stir in the chocolate chips.
  • BAKE: Divide the mixture evenly among 9 muffin cavities and place a few (3-4) extra chocolate chips on top if desired. Bake for 19-24 minutes or until the tops of the muffins look dry (not gooey) (My oven takes 23 minutes). Remove and allow to cool for 3-4 minutes and then remove them from the muffin pan onto a cooling rack.
  • STORAGE: Store muffins in an airtight container at room temperature. Muffins are best when used within 1-2 days.

Video

Recipe Notes

Note 1: Use high-quality pumpkin that isn’t overly watered down (I prefer Libby’s). Make sure to use pure canned pumpkin, not pumpkin pie filling. Note that this recipe only uses 1 cup of pumpkin, not the entire can!
Note 2: If you aren’t used to healthier baked goods, use 4-6 tablespoons brown sugar in these muffins. I typically use a packed 4 tablespoons (1/4 cup)
Note 3: Oat flour is just old-fashioned or quick oats that have been blended in a food processor or blender until they reach the consistency of flour. Make sure to measure the oat flour AFTER blending, not before. Level the measuring cups after being completely filled with oat flour (don’t loosely measure).
Storage: Store muffins in an airtight container. Best within 1-2 days.
Freezing: Freeze in a single layer, then transfer to a bag or container. Freeze up to 3 months. Thaw at room temp or microwave before serving.

Nutrition

Calories: 219kcal | Carbohydrates: 32g | Protein: 6g | Fat: 7g | Saturated Fat: 5g | Cholesterol: 21mg | Sodium: 166mg | Potassium: 249mg | Fiber: 3g | Sugar: 10g | Vitamin A: 4121IU | Vitamin C: 1mg | Calcium: 75mg | Iron: 2mg

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

Meet Chelsea


Hello, and welcome to Chelseaโ€™s Messy Apron! Iโ€™m Chelsea, the recipe developer, food photographer, and writer behind the site. Iโ€™m passionate about creating simple, reliable, and delicious recipes that anyone can make.

Thanks for stopping byโ€”I hope you find something delicious to make!

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4.82 from 50 votes (5 ratings without comment)

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184 Comments

  1. Heather says:

    Hi Chelsea! I made these muffins today and they came out awesome! I do have one question though…do I use liquid or dry measurement for the pumpkin? I used dry measurement and it seems they came out a bit too moist. Or, maybe I should have baked them just a little longer?
    Heather

    1. chelseamessyapron says:

      Thanks so much Heather! So glad you enjoyed them ๐Ÿ™‚ The baking time may be different based off of your altitude or differences in ovens. If they are too moist maybe try baking them a little longer or adding a bit more oat flour ๐Ÿ™‚

  2. Cammie says:

    5 stars
    Made these yesterday with some friends. We inhaled the entire batch before they even had time to cool. None of us could believe there were so many healthy ingredients with how tasty these are. Definitely making these again soon! Thank you!!

    1. chelseamessyapron says:

      Haha! ๐Ÿ™‚ So great to hear it!! Thanks for your kind comment! ๐Ÿ™‚

  3. Angela says:

    2 stars
    I made these last night and yes, they are not much to look at ๐Ÿ™‚ but they are tasty…I went by the 114 cals as well as I’m tracking on MFP…I plunked the ingredients in to the MFP calculator this morning and I’m so sad to say that they came out to 199 cals per muffin !!!!

    I used pure pumpkin puree which is super low is calories but the oat flour jacked up the calories !!! I too used 1/2 cup of mini chocolate chips…the Enjoy Life brand that are dairy free, nut free etc ….I am so disappointed that the calories are so high…Im sorry to say but they just aren’t worth 199 calories. I hate to throw the rest away so I’ll be working out extra hard this week to make up eating some. Too bad my husband doesn’t like pumpkin.

    1. chelseamessyapron says:

      I don’t believe 199 calories per muffin is accurate. There have been lots of people calculate the nutrition facts on these muffins if you read through the comments and they tend to come out about 100-145 per muffin. (I always get You can also freeze them if needed!) I get that they are each 102 calories on this site: http://www.caloriecount.com/cc/recipe_analysis.php

      1. Jennifer Palfy says:

        to make this recipe even healthier I used maple syrup instead of brown sugar.

  4. Olivia says:

    My friend made these and they were absolutely delicious! I was wondering if they would work with almond flour instead of oat flour? Thank you!!

    1. chelseamessyapron says:

      So great to hear! Thanks for the comment ๐Ÿ™‚ I can’t say for sure since I’ve never used almond flour (and don’t have tons of experience with it), but I don’t see why the substitution wouldn’t work. Sorry to not be of more help!

  5. Robin says:

    Hi Chelsea,
    I made these pumpkin muffins and the taste was great, but the texture reminded me more of a baked oatmeal (only with ground oats), they are not as light and airy as a muffin. I have yet to find a baked oatmeal recipe that tastes as “pumpkiny” as this, so I was wondering what would happen if I used regular old fashioned oats instead of the ground oats in this recipe? Would I need to adjust the amount and use more oats? I was thinking they would make fun little baked oatmeal cups. Thoughts?

  6. Alia says:

    Hello! I tried making these, but they did not rise ๐Ÿ™ After some other pumpkin recipe fails, I realized it must be the pumpkin puree I used, as my rising agents were fresh. Do you have any suggestions for what brands of pumpkin puree to use, or which one you used? I used E. D. Smith, but for some reason, it only seemed to work in recipes requiring white flour, as opposed to the oat flour in this one, and ww pastry flour in another. The batter didn’t look overly wet either, so I’m not sure what went wrong. I’m also sure I followed the recipe exactly. Any advice? ๐Ÿ™‚

    1. chelseamessyapron says:

      Oh no! I haven’t ever had a problem with these not rising so I wonder if it is the pumpkin puree you are using if it is having problems in other recipes as well! I generally use Libby’s 100% pure pumpkin (this has the least amount of extra liquid added in my opinion/experience) and occasionally will use the great value brand that Wal-Mart makes. Both have been used and worked great in these muffins. I’m also wondering, perhaps altitude could make a difference? Yours may need to bake for longer if they are deflating. If they are rising during the baking and then deflate after you pull them out of the oven they may not have baked long enough. I hope this helps!

  7. Jackie says:

    5 stars
    I made these yesterday. Used coconut sugar, was super careful not to over-stir. They were fantastic! Can’t get over how healthy/easy/tasty they are. Making them again for sure!!

    1. chelseamessyapron says:

      So glad to hear coconut sugar was good in these — I’ll have to try that next time ๐Ÿ™‚ Thanks for your kind comment! Glad you enjoyed these!

  8. Emily O'Connor says:

    5 stars
    Discovered some canned pumpkin in the back of my pantry and had to find a way to use it! These are amazing – so moist. I should have blended my oats a little longer than I did, my muffins came out a little more textured than I was hoping. Noted for next time. Thanks for sharing!! ๐Ÿ™‚

  9. candice says:

    hi chelsea, thanks for the recipe… looks great…. exactly what i am looking for right now actually ๐Ÿ™‚
    1 question though…. why no muffin liners?….. i dont yet own a muffin pan (soon) … so i usually just use the liners on their own in a tray… hope to hear from you … thanks ๐Ÿ™‚

  10. Nicole says:

    Hi Chelsea,

    I’ve made some of your recipes, they’re great! I love anything pumpkin. I’ve wanted to make these muffins…today was the day! To make the recipe even healthier, I used coconut sugar in place of honey, apple sauce in place of brown sugar and a flax egg. I had enough batter for twelve muffins! I wasn’t sure how good they would be basd on how they looked. They are delicious. YUM!

    1. chelseamessyapron says:

      SO great to hear! I love all your healthy swaps and the changes you made and am so glad to hear they were delicious for you ๐Ÿ™‚ Thanks for the comment!