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. Kelly says:

    Healthy muffins with chocolate? Definitely count me in! Love that they are gluten free too – they sound fantastic girl! Aaw, and hope your lil guy is feeling better too.

  2. Monet says:

    What a great and healthy pumpkin recipe to start off the fall season!

  3. Gayle says:

    You just combined my two faves in a skinny muffin! This sounds perfect, Chelsea! Can’t wait to try these cuties out. Pinned!

  4. Michele says:

    Chelsea these sound delicious! I made my own GF version last weekend but with pecans instead of chocolate chips, I love how dense the pumpkin makes the muffins ๐Ÿ˜‰ yours look delicious! Pinned!

  5. Anna @ Sunny Side Ups says:

    Yum! I love how healthy these are, and especially that they’re gluten free so that I can make them for my family! ๐Ÿ™‚ These are a must try–and soon! ๐Ÿ™‚

  6. Ashley says:

    I could definitely enjoy the heck out of these muffins! They sound awesome – I love pumpkin and dark chocolate together!

  7. Dorothy says:

    I’m totally making these!! They look amazing. Pinned!

  8. Amanda @ .running with spoons. says:

    Girl! Omg I totally had to laugh when I saw these because I whipped up a batch of flourless chocolate chip pumpkin muffins this weekend myself. Great minds? ๐Ÿ˜€ There’s just something about this time of the year, and the combination of pumpkin and chocolate, that BEGS for it to be made, though. Pinned ๐Ÿ™‚

  9. Julie says:

    These look perfect for enjoying a treat without the guilt! And great tips for making muffins turn out just right.

  10. Jess says:

    These look fantastic! And just perfect for conquering those sweet cravings without toooooo many calories! I will have to try!