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. R says:

    5 stars
    I never comment on recipes (and I mean never!), but I’m making an exception because this recipe is AMAZING! These are the BEST muffins I’ve ever made! And I don’t mean just the best pumpkin muffins – these are the best of all the muffins I’ve made. I’ve used a lot of different recipes, but this is by far my favorite. Thank you for sharing this recipe with us!!

    1. chelseamessyapron says:

      Thank you so much for such a sweet comment! I feel so honored ๐Ÿ™‚ I am thrilled you enjoyed these!!

  2. Mary says:

    5 stars
    I made these last night and they are delicious, dense and moist!
    I accidentally added the entire can of pumpkin, so I doubled the oat flour. I will be making these again.

    1. chelseamessyapron says:

      Glad to hear these still worked and you enjoyed them! ๐Ÿ™‚

  3. Emy says:

    5 stars
    I made these for my 2 year old because he is a very picky eater & they were a big hit! I have to sneak in veggies and fruits wherever I can so I decided to modify the recipe the second time around. I used 1/2 cup of pumpkin and blended 1/2 of a zucchini & a mushy banana. I also added 1/4 cup of quick oats in addition to the oat flour to help soak up the extra mixture. The result was a very delicious cupcake that my 2 year old can have for breakfast, lunch or dinner! Thank you Chelsea!

    1. chelseamessyapron says:

      LOVE all your healthy additions and glad you enjoyed these! Thanks for sharing!

  4. Urmila McClure says:

    Hi Chelsea, was just wondering if this recipe would do ok baking in a bundt pan? Or should I just do as a cup cake?

  5. Dawn says:

    Hi, I love the ingredients in this recipe though when I made them they were waaaaay too wet. Not sure why, maybe the size of the can of pumpkin. The recipe doesn’t specify, so I used 798 ml. Thinking maybe I should have used the small can. Will try again, ate them anyway ’cause they tasted great!

    1. chelseamessyapron says:

      You aren’t supposed to use an entire can at all. The recipe indicates only using 1 cup. Hope that helps!

  6. celeste says:

    Chelsea –do you know how many calories and carbs are in these awesome muffins? A friend made some the other day and shared with me…and now I want more!!

    1. chelseamessyapron says:

      I don’t know the carbs sorry Celeste! You can plug in the ingredients to an online calorie counter and that should give you the numbers. I think a few readers have calculated the calories and they come out to about 120 calories per muffin!

  7. Ruth says:

    4 stars
    These are fantastic. I made a double-batch yesterday, and I’m going to make another batch today to bring to a friend. I have four picky eaters at home, and all four loved these muffins, AND, I felt good about the healthy ingredients. Thank you for sharing this!

    1. chelseamessyapron says:

      Yay! SO great to hear!! Thanks for taking the time to leave a comment Ruth and glad you all loved these! ๐Ÿ™‚

  8. Emma says:

    5 stars
    Wow – I was not expecting these to be so good, but they truly are! I just whipped them out of the oven and cooled them down long enough to enjoy my first taste. Delicious! I will be making these regularly. Thank you!

  9. Marg says:

    can you tell me what size of can if pumpkin you used? I can get 2 different sizes so want to make sure I use the right one. Thanks

    1. chelseamessyapron says:

      I don’t use an entire can, just one cup as the recipe indicates! Hope that helps! ๐Ÿ™‚

  10. Annesha Goswami says:

    These look amazing!!! Do you think I can also make them with sweet potato instead of pumpkin? I <3 sweet potatoes but would they be compatible?

    1. chelseamessyapron says:

      I haven’t tried sweet potato, but I don’t see why that wouldn’t work! I’d love to hear the results if you try it! ๐Ÿ™‚