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These Healthy Pumpkin Muffins are made with whole wheat flour, pumpkin puree, and maple syrup for a naturally sweetened treat. Perfect for breakfast or snacking, this pumpkin muffin recipe is moist, flavorful, and ready in just 30 minutes!

healthy pumpkin muffins baked and on the cooling rack.


 

Quick Recipe Overview

healthy pumpkin muffin dough into the tin with oats on top.

WHAT: A healthier version of sugar-laden muffins — whole wheat and oats, pumpkin puree, and maple syrup for a touch of sweet.

WHY: The texture is soft and moist, and the pumpkin and spices add a rich, warm flavor that’s perfect for fall. Plus they’re super easy to make and ready in about 30 minutes.

HOW: As simple as mixing the wet ingredients, adding the dry, and baking!

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Table of Contents

Why I Love Making These Healthy Pumpkin Muffins

I always love finding ways to make my favorite treats a little healthier, and these pumpkin muffins do not disappoint! The pumpkin adds natural sweetness and moisture, making these muffins not only delicious but also packed with nutrients.

These muffins are made entirely from scratch but only take about 30 minutes to make, which is perfect for a quick breakfast or snack. You can enjoy them on their own, spread with a little almond butter, or paired with a warm cup of tea.

Serve these healthy pumpkin muffins with a recovery smoothie, eggs, or a spread of nut butter for a balanced and satisfying meal.

Feautured Review

Emily ⭐️⭐️⭐️⭐️⭐️

August 21, 2018

These were really good. I added 1/2 cup of semi sweet chocolate chips. Very moist, but not squishy, just the right amount of sweetness. The oats give great texture. I used muffin liners and they pulled off perfectly. I’ll be keeping this recipe for sure!

Melissa in her kitchen smiling in front of the starting ingredients for the chicken the quinoa salad and skillet chicken on the wood block in front of her

🩷 Melissa

These healthy pumpkin muffins have become a fall staple in my kitchen, and I hope they become one in yours too!

Whether you enjoy them warm from the oven with a pat of butter, pack them in lunchboxes, or serve them at brunch, they’re sure to be a hit.

The combination of whole wheat flour, warming pumpkin spice, and natural maple syrup creates something truly special – wholesome enough for breakfast, delicious enough for dessert!

Ingredient Notes

Whole Wheat Flour: Adds a bit of heartiness and extra fiber to the muffins. You can use whole wheat pastry flour or half whole wheat and half all-purpose.

Pumpkin Puree: Be sure to use pure pumpkin puree, not pumpkin pie filling! If you want to use up the whole can of pumpkin in one go, just double this recipe for 24 regular-sized muffins.

Maple Syrup: Provides natural sweetness and complements the pumpkin flavor.

Coconut Oil: A good oil for those wanting to stay away from other oils, though you can use any light-flavored oil in this recipe, such as canola or vegetable oil.

healthy pumpkin muffins in portioned ingredients.

See the recipe card below for full information on ingredients and quantities.

Feautured Review

Megan ⭐️⭐️⭐️⭐️⭐️
April 7, 2018

These were great! Nice and moist, with great flavor. Thanks for the recipe!

healthy pumpkin muffins baked into the tin.
4.72 from 7 votes

Healthy Pumpkin Muffins

By: Melissa Griffiths
These Healthy Pumpkin Muffins are made with whole wheat flour, pumpkin puree, and maple syrup for a naturally sweetened treat. Perfect for breakfast or snacking, this pumpkin muffin recipe is moist, flavorful, and ready in just 30 minutes!
Prep: 10 minutes
Cook: 25 minutes
Total: 35 minutes
Servings: 12 muffins
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Ingredients 

  • ⅓ cup melted coconut oil
  • ½ cup real maple syrup
  • 2 eggs
  • 1 cup pumpkin puree
  • ¼ cup milk of choice, (I used almond milk.)
  • 1 teaspoon vanilla extract
  • 1 teaspoon baking soda
  • ½ teaspoon salt
  • 1 teaspoon cinnamon
  • 1 ¾ cups whole wheat pastry flour or regular whole wheat flour
  • ⅓ cup old-fashioned oats, plus more for sprinkling on top

Instructions 

  • Preheat oven to 325°. Grease a 12-cup muffin tin well and set aside.
  • In a medium bowl, add the melted coconut oil, pure maple syrup, egg, pumpkin puree, milk and vanilla. Whisk to combine well.
  • In a large bowl, add the soda, salt, cinnamon, flour, and oats. Stir to combine.
  • Add the wet ingredients to the dry ingredients and stir until just combined. Don't over mix here.
  • Divide the batter among the 12 muffin cups. Sprinkle with additional oats.
  • Bake for 22-25 minutes, or until a toothpick inserted into the center comes out clean and the muffins spring back when lightly touched.
  • Let the muffins cool for 5 minutes in the pan and then remove and allow them to cool on a wire rack. Enjoy warm or at room temperature.

Notes

Extra Muffins: If you want to use up the whole (15 ounce) can of pumpkin in one baking session, just double this recipe and add the entire can instead of 1 cup. You’ll get 24 muffins, perfect for a make ahead prep.
Chocolate-y Muffins: If you want these to taste more like dessert, try adding in 1 cup of good chocolate chips. Pumpkin and chocolate are always a good idea in my book!
No Sticking: Grease your muffin tin really well with coconut oil or cooking spray, making sure to get into all the corners. You can also use paper muffin liners for easy removal, though I find greasing the pan gives you those beautiful golden edges.

Nutrition

Serving: 1 of 12 muffins, Calories: 183kcal, Carbohydrates: 25g, Protein: 4g, Fat: 8g, Saturated Fat: 6g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Trans Fat: 0.003g, Cholesterol: 27mg, Sodium: 202mg, Potassium: 166mg, Fiber: 3g, Sugar: 9g, Vitamin A: 3219IU, Vitamin C: 1mg, Calcium: 34mg, Iron: 1mg
Like this recipe? Rate and comment below!

How To Make Healthy Pumpkin Muffins

healthy pumpkin muffins in portioned ingredients.

Step 1: Combine the dry ingredients in a bowl and mix.

clear mixing bowl in the process of making healthy pumpkin muffins.

Step 2: Combine the wet ingredients in a bowl and mix well. Then add the dry ingredients to the wet and mix just until the dry is incorporated

healthy pumpkin muffin dough into the tin.

Step 3: Divide the batter among the 12 muffin cups.

healthy pumpkin muffin dough into the tin with oats on top.

Step 4: Sprinkle with additional oats.

healthy pumpkin muffin dough into the tin with oats on top.

Step 5: Bake for 22-25 minutes, or until a toothpick inserted into the center comes out clean and the muffins spring back when lightly touched.

healthy pumpkin muffins baked and on the cooling rack.

Step 6: Let the muffins cool for 5 minutes in the pan and then remove and allow them to cool on a wire rack. Enjoy warm or at room temperature.

FAQs for Healthy Pumpkin Muffins

Can I use fresh pumpkin instead of canned?

If you prefer using fresh pumpkin, simply roast it and puree it until smooth. Keep in mind that fresh pumpkin may have a slightly different moisture content, so you might need to adjust the amount of flour.

Can I add mix-ins to these muffins?

Yes! Feel free to add your favorite mix-ins like chopped nuts, dried cranberries, or dark chocolate chips. Just be sure not to add too much, as it could affect the baking time and texture.

Can I make these gluten free pumpkin muffins?

Make these gluten-free by substituting the whole wheat flour with your favorite gluten free flour blend (one that’s designed for 1:1 substitution). Bob’s Red Mill and King Arthur both make excellent options. The texture will be slightly different but still delicious!

healthy pumpkin muffins baked and on the cooling rack and sliced open with butter inside.

My Best Tips for Making Pumpkin Muffins

  • Swap Flours: You can substitute half of the whole wheat flour with oat flour for a different texture and added flavor.
  • Don’t Over-Mix: Be careful not to overmix the batter; stir until just combined to keep the muffins tender.
  • Extra Sweetness: For an extra touch of sweetness, sprinkle a little cinnamon sugar on top of the muffins before baking.
  • Fall Flavor: If you prefer a more robust spice flavor, increase the amount of cinnamon, nutmeg, or ginger to your taste.

Serving Ideas

These pumpkin muffins are a great grab-and-go breakfast or snack. Enjoy them warm with a little nut butter or simply on their own.

They’re also perfect for meal prepping since they store very well.

Storage & Reheating Tips

Pumpkin muffins can be stored in an airtight container on the counter for up to 3 days or in the fridge for up to 5 days.

For longer storage, you can freeze these muffins. Simply place them in a single layer on a baking sheet to freeze individually, then transfer them to a freezer-safe bag or container. They’ll keep well for up to 3 months.

To enjoy, just thaw at room temperature or warm them up in the microwave.

healthy pumpkin muffin dough into the tin with oats on top.

More Yummy Muffin Recipes To Try

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4.72 from 7 votes

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Recipe Rating




20 Comments

  1. Chris says:

    5 stars
    Gave it 5 stars with my changes; it’s a great base recipie. I used: pancake syrup cuz maple is too expensive; regular canola oil cuz that’s what we have; white flour and 1/3 cup whole wheat; added about 1/4 cup chopped apple and dried cranberries. It’s really good, “healthy…er” and just sweet enough. Took a few tries to get it where the whole family gave it 5 stars.

    Reply