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. Natalie says:

    These look delicious and will definitely be making them soon! Just wanted to clarify, your baking time next to the prep time says 11 minutes, however the instructions say 18-22 minutes (which I assume is the correct time). Could you tell me which one it is? Thanks!

    1. chelseamessyapron says:

      Hmm not sure why it says 11 minutes, I’ll update that ๐Ÿ™‚ Yes 18-22 minutes and then check with a toothpick (if it comes out clean they should be done!)

  2. Lindsey says:

    The calorie count is wrong!!!!!

    It is 82 calories per muffin if decided into 9 muffins!

    I thought his was to good tone true so checked the recipient against a calorie counter for recipes. And got a much different calorie count. (Caloriecount.com)

    1. chelseamessyapron says:

      Yes if you read the other comments, it’s been updated. The pumpkin calorie count was off throwing everything else off. The post has been updated.

  3. Lily says:

    Sounds delicious! Can I use regular flour instead of oat flour? And if so, would the measurement change? Thanks!

    1. chelseamessyapron says:

      I haven’t actually tried regular flour in these ever so I’m not sure. I believe it would be the same, but can’t say for sure without further recipe testing. I do have a new pumpkin recipe on my site (search: pumpkin muffins) that use regular or white whole wheat flour. You could make those and add chocolate chips to them ๐Ÿ™‚

      1. Lily says:

        Thank you so much, i’ll give them a try! Craving a late-night snack.

  4. stacey says:

    Probably a dumb question, but is canned Pure Pumpkin Puree what we use here? Or is there something different I should be looking for?

    1. chelseamessyapron says:

      Not a dumb question ๐Ÿ™‚ Yep just canned pumpkin puree ๐Ÿ™‚ I recommend a good quality (not water-y) brand for best results! ๐Ÿ™‚

      1. stacey says:

        Great, thanks! My 4-YO son is VERY excited to make these with me.

        1. chelseamessyapron says:

          Sounds like fun!! I hope you both love them ๐Ÿ™‚

  5. Kelsey says:

    4 stars
    These muffins were delicious and super moist, just as promised. The only downside, as others have commented, the stated nutrition is incorrect. When I made these each muffin (I divided them into 8) was 115 Calories, 2g fat, 22g carbs, 3g protein. This is not for all the muffins as stated in the blog, but for each one. The honey alone is 128 Calories! I even substituted 3 Tbsp of egg whites for the whole egg and only used 1/4 cup of chocolate chips. I will be making again, but will make a few adjustments.

    1. chelseamessyapron says:

      So glad you enjoyed them!! Yes the calorie count will change depending on how many muffins you make and if you put in more/less batter per muffin! ๐Ÿ™‚

  6. Scout says:

    5 stars
    Fantastic! I made them for my bookclub and sent the recipe to everyone after they were gobbled down! I’m making another batch for the family tonight. Excellent recipe!

    1. chelseamessyapron says:

      Yeah!! SO great to hear!! Glad everyone enjoyed these ๐Ÿ™‚ Thanks for the comment!

  7. Sarah says:

    I’ve made these twice and am planning on making them again this weekend! They are AMAZING. Just a heads up, I used the large muffin tins and was only able to fill up four, at 3/4 the way full. I recommended doubling or tripling the recipe! Thanks for these- we adore them!

    1. chelseamessyapron says:

      Yay!! So glad to hear you’ve been enjoying these! ๐Ÿ™‚ And I love the idea to use large muffin tins — yum!! Thanks for the comment!

  8. Kayla says:

    I love these muffins! They are easy to make and taste delicious! Thank you for sharing this recipe!! I can’t wait to try more of your recipes!!

    1. chelseamessyapron says:

      That’s great to hear, I am thrilled you’ve enjoyed these muffins!! I hope you enjoy the next recipe you try! ๐Ÿ™‚ Thanks for the comment!

  9. Jessica says:

    5 stars
    Made these about an hour ago and they are FANTASTIC. I was really impressed. They are easy to make and super delicious.

    1. chelseamessyapron says:

      Yeah!! So great to hear!! I’m glad you loved these ๐Ÿ™‚ Thanks for the comment!

  10. Gillian says:

    Just made these! They are so good! LOVING how healthy they are…and planning more ways to use pumpkin! Definitely an underrated vegetable, health wise. I even subbed your oat flour for almond flour to make these grain free. ๐Ÿ™‚ Thanks! I featured these on my tumblr today.

    1. chelseamessyapron says:

      So glad to hear you enjoyed these!! ๐Ÿ™‚ Thanks for the comment!