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.

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 canned pumpkin, honey, brown sugar, vanilla, and egg in one bowl. In another, mix salt, baking soda, baking powder, cinnamon, nutmeg, pumpkin pie spice, and oat flour.
  3. Combine & Bake: Merge 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
  • 2 -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).

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


Hi there! Iโ€™m Chelseaโ€“the recipe developer, photographer, writer, and taste tester behind Chelseaโ€™s Messy Apron (although my little ones help me out quite a bit with the taste testing part!). I LOVE getting creative in the kitchen and then posting my creations here for you to enjoy.

Thanks again for stopping by!

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4.82 from 50 votes (5 ratings without comment)

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184 Comments

  1. Elle Bishop says:

    5 stars
    Awesome recipe!!! I wanted to try it but didnโ€™t have chocolate chips so I used butterscotch chips and they turned out amazing! Rave reviews from everyone who tried them!!

    1. Chelsea Lords says:

      Yay! So happy to hear! Thanks Elle! ๐Ÿ™‚

  2. Joan says:

    These are great! I did add some applesauce – about 1/4 c. for more moisture. I would love to see the nutritional info.

  3. Rachel says:

    4 stars
    I’ve made these muffins several times, and they’re delicious, but they always come out a bit too dense, despite my efforts to mix as little as possible. Have you tried putting the wet into the dry, instead of vice versa?

    1. Chelsea Lords says:

      Hmm, you can certainly do that. Are you making any ingredient changes in the recipe?

      1. Rachel says:

        A very belated response, but nope! I follow the recipe as written.

        I did try putting the wet into the dry today, and I didn’t see a noticeable difference in terms of texture. I might also be overbaking them, so I’m going to try another batch tomorrow for less time and see how it goes…

        P.S. Happy holidays!

  4. Katie says:

    What sort of choc chips did you use? I couldn’t find any so tried to make my own with a dark choc bar. They have come out a little bitter, it was a 70% coco it was all that was in the shop. Made these again a few years ago and my husband still talks about how yummy they were. Thanks!

    1. Chelsea Lords says:

      So happy you’ve enjoyed! I use dark chocolate ๐Ÿ™‚

  5. Monica says:

    5 stars
    Just made these muffins last night for the first time and they are absolutely amazing!! So so delicious! The perfect pumpkin muffin recipe – flavourful and great texture! What a perfect recipe. Iโ€™ll be making another batch today to bring to my sister. Thank you so much for sharing ๐Ÿ™‚

    1. Chelsea Lords says:

      So happy to hear these were a hit ๐Ÿ™‚ Thanks so much for the comment Monica! ๐Ÿ™‚

  6. Cindy laban says:

    Can you please post the nutritional info for these healthy choc chip pumpkin muffins? I’m on WW points plus and need to figure out point value

  7. Karen says:

    I would like to know if this can be made without the egg? Can a flax or chia egg be used instead? Or anything else to help bind everything? Has anyone tried this?

    1. Mindy says:

      5 stars
      This is one of the few Pinterest recipes that I find myself making over and over. My daughter loves them in her lunches. Over time, I gave up making oat flour and now I just use 1 cup of gf flour instead. It works great. I also freeze them and they defrost well. Thx for for a great healthy snack recipe that my kid will actually eat!

      1. chelseamessyapron says:

        Ahh I’m so happy to hear this! And it’s great to know that gf flour works well too! Thanks so much for your comment Mindy! ๐Ÿ™‚

  8. Andrea says:

    Hey there!! Iโ€™m sure this question was already asked but do you think almond flour could be used instead of oat?? ๐Ÿ™‚

  9. Jenna says:

    5 stars
    I donโ€™t bake much, but when I do I make these because my kiddos beg for them!!!

    Iโ€™ve added flax at time for bonus nutrition!

    1. chelseamessyapron says:

      LOVE hearing that! Thanks for the comment Jenna ๐Ÿ™‚

  10. Sonlla says:

    Iโ€™m a little late to this party, but what are the macros per muffin???