Healthy Pumpkin Muffins

Healthy Pumpkin Muffins are made with whole wheat flour, Warm spices, pumpkin, coconut oil, and sweetened with pure maple syrup. These easy and delicious muffins make a great fall breakfast or snack!

Pumpkin Muffins

Pumpkin Recipes

I love baking with pumpkin and make quite a few decadent pumpkin recipes. For example, have you tried my Pumpkin Chocolate Chip Cookies, Pumpkin Sheet Cake, or Pumpkin Bundt Cake? They are all SO good and worth every single bite, but I thought it was time I made a healthy pumpkin recipe. Let me introduce you to my Healthy Pumpkin Muffins. They are on the healthier side, but you will never know it because they are super delicious. So delicious that my boys called them pumpkin cupcakes at first…ha! I fooled them:)

Healthy Pumpkin Muffins

How to Make Healthy Pumpkin Muffins

I promise this muffin recipe is super simple and you won’t even know they are on the healthy side because they are SO delicious! To make healthy pumpkin muffins, you need a few key ingredients:

  • White whole wheat flour or whole wheat flour. I like to use white whole wheat flour because it is lighter in color and texture. My boys don’t even know they are eating whole wheat muffins. Regular whole wheat flour will work well too. If you want to make gluten-free pumpkin muffins, you can use all-purpose gluten-free flour, I like Cup4Cup or Bob’s Red Mill.
  • Pumpkin. This one is obvious, but make sure you use pure pumpkin puree and not pumpkin pie filling. The pumpkin is a healthy addition to the muffins and keeps the muffins super moist without adding any fat or sugar.
  • Coconut oil. Instead of using butter, I use melted coconut oil.
  • Pure maple syrup. The muffins are sweetened with pure maple syrup, there are no refined sugars in this pumpkin muffin recipe. Make sure you buy PURE maple syrup, you want the good stuff! The maple flavor is so good and adds the perfect amount of sweetness.
  • Almond milk. I use unsweetened vanilla almond milk in this recipe because there are no added sugars. You can use regular milk or buttermilk if you wish.
  • Eggs. You will need two large eggs to make the muffins. I love the protein they add. If you need the recipe to be vegan, you can use a flax eggs.
  • Spices. Adding in ground cinnamon, ginger, nutmeg, and cloves gives the muffins a ton of flavor! The warm fall spices compliment the pumpkin perfectly!

Muffin Tips

I love this pumpkin muffin recipe because they are so easy to make. You don’t even need a mixer. There are a few key tips I want to share for baking muffins.

  • Make sure you line the muffin pan with paper liners or grease the muffin cups with nonstick cooking spray.
  • Measure all of your dry ingredients and put them in a bowl. Use a whisk to combine them all together.
  • Make sure all of your wet ingredients are at room temperature.
  • When you combine the dry ingredients and the wet ingredients, don’t over mix the batter. If you do, you will have dense, tough muffins and they won’t rise as much.
  • Fill the muffin cups about 3/4 of the way full.
  • I like to sprinkle the muffins with turbinado sugar before they go in the oven. The sparkly, sugary crunch is always a nice finishing touch!
  • Don’t over bake the muffins. Take them out with a toothpick inserted into the center comes out clean.
  • Let the muffins cool before eating.

Mix it Up

I love a plain pumpkin muffin, but if you want to mix things up you can add the following ingredients.

  • 1 cup dark chocolate chips or mini chocolate chips. Yes, they are healthy pumpkin muffins, but I won’t tell if you add chocolate. Chocolate is always a good idea and SO good for mental health:)
  • 1 cup dried cranberries or raisins
  • 1 cup chopped walnuts or pecans
  • You can also top the muffins with pepitas or old-fashioned oats.
  • If you are feeling fancy, you can glaze the muffins with a maple or orange glaze.

Can You Freeze Pumpkin Muffins?

YES! I love making these muffins because they do freeze well. Let the muffins cool completely and then put them in a freezer bag or freezer container and freeze for up to 2 months. When ready to eat, you can let them defrost on the counter or you can pop them into the microwave for about 30 seconds. I love having a stash in the freezer for busy mornings. The boys love grabbing one before school.

Perfect for Breakfast or Snack Time

Are you ready to bake some pumpkin muffins? I sure hope so! These healthy muffins make a great breakfast. You can make them on a lazy weekend morning or you can whip up a batch during the week so you can grab a muffin and go! There is no wrong morning to make and enjoy pumpkin muffins. They also make a great fall snack. Enjoy with a glass of milk and you are all set!

If like these pumpkin muffins, you might also like:

Pumpkin Muffins Recipe

4.89 from 9 votes
Print Review

Healthy Pumpkin Muffins

4.89 from 9 votes
These easy pumpkin muffins are a fall favorite for breakfast or snack time. You will never know they are healthy because they are SO delicious!
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Course Breakfast
Cuisine American
Servings 12 muffins


  • 1 3/4 cups white whole wheat flour or whole wheat flour
  • 1 teaspoon baking soda
  • 1 1/2 teaspoons ground cinnamon
  • 1/2 teaspoon kosher salt
  • 1/2 teaspoon ground ginger
  • 1/4 teaspoon ground nutmeg
  • 1/8 teaspoon ground cloves
  • 1 cup pumpkin
  • 2 large eggs at room temperature
  • 1/2 cup pure maple syrup
  • 1/3 cup coconut oil melted and cooled to room temperature
  • 1/4 cup unsweetened vanilla almond milk at room temperature (or milk of your choice)
  • 1 1/2 teaspoons pure vanilla extract
  • Turbinado sugar for sprinkling on muffins, optional


  1. Preheat oven to 350 degrees F. Line a 12-cup muffin pan with paper liners or grease the cups with nonstick cooking spray. Set aside.
  2. In a medium bowl, whisk together the flour, baking soda, cinnamon, salt, ginger, nutmeg, and cloves. Set aside.
  3. In a large bowl, combine the pumpkin, eggs, maple syrup, cooled coconut oil, milk, and vanilla extract. Stir until smooth.
  4. Add the dry ingredients to the wet ingredients and stir with a spatula until just combined. Don't over mix.
  5. Pour the muffin batter evenly into the prepared muffin cups. Sprinkle the muffins with turbinado sugar, if using. Bake for 20-24 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  6. Let the muffins cool and enjoy!
Nutrition Facts
Healthy Pumpkin Muffins
Amount Per Serving
Calories 163 Calories from Fat 63
% Daily Value*
Total Fat 7g 11%
Saturated Fat 5g 25%
Cholesterol 27mg 9%
Sodium 206mg 9%
Potassium 92mg 3%
Total Carbohydrates 22g 7%
Dietary Fiber 1g 4%
Sugars 8g
Protein 3g 6%
Vitamin A 17.3%
Vitamin C 1.1%
Calcium 4.1%
Iron 3.6%
* Percent Daily Values are based on a 2000 calorie diet.
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