Healthy Pumpkin Muffins

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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

Healthy Pumpkin Muffins

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!
4.89 from 9 votes
Prep Time
15 minutes
Cook Time
20 minutes
Total Time
35 minutes
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*
Fat 7g11%
Saturated Fat 5g25%
Cholesterol 27mg9%
Sodium 206mg9%
Potassium 92mg3%
Carbohydrates 22g7%
Fiber 1g4%
Sugar 8g9%
Protein 3g6%
Vitamin A 865IU17%
Vitamin C 0.9mg1%
Calcium 41mg4%
Iron 0.6mg3%
* Percent Daily Values are based on a 2000 calorie diet.

healthy pumpkin muffins, pumpkin muffins

Maria Lichty

I’m Maria and my husband is Josh. We share a love of cooking, baking, and entertaining. We enjoy creating recipes that are simple, fresh, and family friendly. We love sitting around the table with good food, good conversation, and good friends and family! Our kitchen is always open!
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CommentsLeave a reply

  1. These look delicious. I am wondering if I can substitute light olive oil for the coconut oil? I have read and heard so much lately about how unhealthy coconut oil is…the the initial hype about benefits  has now been disproved. 

    1. In most baked goods you can substitute flaxseed for eggs (called a “flax egg”). 1 Tbsp ground flax seed + 3 Tbsp water, mixed in a bowl and left to sit for 5 minutes is the equivalent of 1 egg.

    1. I am sure a loaf pan would be just fine. Just add baking time, probably 45-60 minutes, depending on your oven.

  2. Hello! Thank you for sharing the recipe. I’m so wondering if I can bake this in a pound cake pan just like your another pumpkin bread recipe. What temperture and how long should I bake it for???

  3. I liked the recipe but I think 1 teaspoon might be a little too much baking powder – it gives the muffins a metallic after taste.

  4. These sound delicious! I would love to make these!! I would like to get nutritional value—calories, carbs, etc. Thank you!

  5. These were SO delicious. I recently made them for family that came to visit our sweet little new babe and they all RAVED about them. I love that they’re made with whole-wheat flour and coconut oil as well. They came super moist and just perfect.

  6. Hi, can honey be used as a substitute for the maple syrup? And if so,  should I use the same measurement? Thanks so much!

    1. I’m a little late, but what she means is pumpkin puree which is cooked. You can either buy a can of the puree at the store. Or if you’re using fresh pumpkin, you need to cook it in the oven. (Find something online, cooking times vary based on size and type) but its roughly about 45 mins-60 mins. You take the chunks of cooked and cooled pumpkin, and put it in a blender until it becomes creamy and consistent.

  7. These muffins sound delicious, will definitely try them. I just didn’t get the part of the pumpkin. Do you put the pumpkin raw, do you grate it or Fo you cook it first. Sorry never used pumpkin before.

  8. I really like this recipe. I made some changes, which I know is annoying, so I won’t rate your recipe based on that. But I love that you made something that only uses maple syrup for sweetener and the texture is perfect. Though I use sunflower oil. I also increased the sweetness a bit and adjusted the spices. It’s great without vanilla as well! It’s my number one muffin recipe right now! I put a link for it on my website.

  9. Loved these! I made them exactly like the recipe, and added some raisins to the batter before baking. They are absolutely delicious!!

  10. I am super super excited to make these!! This looks awesome and I love all the ingredients you used in this recipe. My friends and family are going to love it. lovely pictures too 😉

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