Healthy Pumpkin Muffins

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These are the best healthy pumpkin muffins ever! They’re tender and moist with a beautiful crumb, naturally sweetened, perfectly spiced and made with whole wheat flour but you’d never guess they’re good for you! This healthy pumpkin muffin recipe is easy to make in 30 minutes, and is a nutritious fall breakfast! 

overhead view of 4 Healthy Pumpkin Muffins on a cooling rack, one cut in half.


Fall baking is my favorite (hello pumpkin bread), but sometimes I want to make lighter versions of my favorite recipes, like these Healthy Pumpkin Muffins. They’re tender and moist with a beautiful crumb, naturally sweetened, perfectly spiced and made with whole wheat flour but you’d never guess they’re good for you! 

This healthy pumpkin muffin recipe is easy to make in 30 minutes – including baking time. You can top them with raw sugar (or not), or add your favorite mix-ins to make them extra-special! Serve them warm with a generous slather of this homemade cinnamon honey butter and you’ll experience breakfast nirvana!

front view of a Healthy Pumpkin Muffin with a bite taken out of it

Healthy Pumpkin Muffin Recipe: Ingredients & Substituions

overhead view of the labeled ingredients in this Healthy Pumpkin Muffin recipe
  • Pumpkin Puree. Be sure to use pure pumpkin puree (not pumpkin pie filling). Fresh or canned both work well. 
  • Salted Butter. Unsalted butter, coconut oil, ghee, etc. can be used in place of salted butter if desired. 
  • Vanilla Greek Yogurt. Any yogurt variety works well in this healthy pumpkin muffin recipe. I prefer vanilla Greek yogurt for the extra protein, flavor and sweetness. I also love using vanilla bean Icelandic yogurt! 
  • Maple Syrup. I’ve used honey in place of maple syrup with great results, however I prefer syrup because the maple flavor screams “fall.” 
  • Eggs. You can use chia or “flax” eggs by combining 2 Tablespoons ground chia seeds or flaxseed meal and 5 Tablespoons warm water and letting it set for 10 minutes, then use in the recipe. The muffins might bake flatter if you do this. 
  • Whole wheat flour. All-purpose, spelt, whole wheat pastry flour, white whole wheat flour, etc. can be used in place of regular whole wheat flour.
  • Pumpkin Pie Spice. Use store bought or make your own with this recipe: homemade pumpkin pie spice.
  • Mix-ins. You can add up to 1 cup of mix-ins of your choice, I will discuss options later in this post! 
6 Healthy Pumpkin Muffins on a wire cooling rack, one has a bite taken out of it

How to Make Healthy Pumpkin Muffins

This healthy pumpkin muffin recipe is easy to make and takes 30 minutes from start to finish. As always, we’ll walk through the recipe step-by-step, and don’t forget to watch the video. 

Begin by combining the whole wheat flour, cinnamon, pumpkin pie spice, baking powder, baking soda and sea salt. Set aside.

Homemade Pumpkin Pie Spice

If you’d like to make your own pumpkin pie spice, use this recipe: homemade pumpkin pie spice. Then use 2 tsp of the mixture in the recipe and save the rest for your other pumpkin recipe endeavors (like this pumpkin pie, paleo pumpkin bread, or pumpkin baked oatmeal).

two overhead photos showing how to make Healthy Pumpkin Muffins

Then, whisk the pumpkin puree, melted butter, yogurt, maple syrup, eggs and vanilla in a large bowl until smooth.

two overhead photos showing how to make Healthy Pumpkin Muffins

Once the wet ingredients are smooth, add the dry ingredients and stir until mixture is smooth and there are no lumps.

Optional: Add mix ins

If desired, add mix-ins of your choice, here are some suggestions: 

two overhead photos showing how to make Healthy Pumpkin Muffins

Bake

Measure 3-4 Tablespoons of batter into each well of a standard muffin in.  If desired, sprinkle the tops of the muffins with raw sugar.

I prefer to generously grease my muffin tins instead of using cupcake liners, but you may bake them either way. 

two overhead photos showing how to make Healthy Pumpkin Muffins

Bake the healthy pumpkin muffins in the preheated oven for 17-20 minutes, or until the tops spring back when touched and a toothpick inserted in the center of the muffins comes out clean or with a few moist crumbs. 

Cool

Let cool in the pan for 2-5 minutes. Then transfer to a wire rack to cool completely, using a spoon or knife to release the sides from the pan and gently remove them.

overhead photo of 6 Healthy Pumpkin Muffins in a muffin tin

Serve

Serve these healthy pumpkin muffins warm with a generous slather of cinnamon honey butter, homemade peanut butter, apple butter, or homemade vanilla almond butter. 

overhead view of 4 Healthy Pumpkin Muffins on a cooling rack, one cut in half.

Store

Store these healthy pumpkin muffins in an airtight container at room temperature for up to 3 days, or in the refrigerator for up to 1 week. 

Freeze

  1. Let muffins cool completely
  2. Transfer to an airtight container or freezer-friendly plastic bag.
  3. Transfer to the freezer and freeze for up to 2 months. 

Reheat

Reheat the healthy pumpkin muffins in one of three ways:

  1. Warm in the microwave for about 40 seconds per muffin. 
  2. Remove from the freezer and let them thaw to room temperature overnight.
  3. Warm in the oven preheated to 325 degrees F for about 5-10  minutes or until warmed through.
front view of a stack of two Healthy Pumpkin Muffins

Healthy Pumpkin Muffins Recipe FAQs

How long are pumpkin muffins good for?

These muffins last for up to 3 days at room temperature, 1 week in the refrigerator, and 2 months in the freezer. Make sure they’re always in an airtight container to prevent drying out.

What goes with healthy pumpkin muffins?

I like to serve these with a slather of homemade cinnamon butter, and on the side of a savory dish like this egg casserole. Always with a warm cup of coffee!

Do pumpkin muffins need to be refrigerated?

They don’t need to be refrigerated but I recommend it because they last longer that way. Reheat for a few seconds in the microwave to restore their from-the-oven warmth and texture.

Can I leave muffins out overnight?

Yes, they are fine when left overnight in an airtight container.

overhead photo of a Healthy Pumpkin Muffin cut in half with butter

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Healthy Pumpkin Muffins

Laura
These are the best healthy pumpkin muffins ever! They’re tender and moist with a beautiful crumb, naturally sweetened, perfectly spiced and made with whole wheat flour but you’d never guess they’re good for you! This healthy pumpkin muffin recipe is easy to make in 30 minutes, and is a nutritious fall breakfast! 
5 from 12 votes
Course Breakfast, brunch
Cuisine American
Servings 12 Muffins
Calories 150
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes

Ingredients 
 

Instructions 

  • Preheat oven to 375 degrees F. Lightly grease a standard, 12-cup muffin tin. Set aside.
  • In a medium bowl, combine whole wheat flour, cinnamon, pumpkin pie spice, baking powder, baking soda and sea salt. Set aside.
  • In a large bowl, whisk together pumpkin puree, melted butter, yogurt, maple syrup, eggs and vanilla until smooth.
  • Add dry ingredients and stir until mixture is smooth and there are no lumps.
  • If desired, add mix-ins (chocolate chips, nuts, seeds, etc.).
  • Measure 3-4 Tablespoons of batter into each cup of the prepared muffin tin. If desired, sprinkle the tops of the muffins with raw sugar.
  • Bake in the preheated oven for 17-20 minutes, or until the tops spring back when touched and a toothpick inserted in the center of the muffins comes out clean.
  • Let cool in the pan for 2-5 minutes. Then transfer to a wire rack to cool completely.
  • Serve.

Video

Notes

Ingredient Substitutions
  • Pumpkin Puree. Fresh or canned both work well. 
  • Salted Butter. Unsalted butter, coconut oil, ghee, etc. can be used in place of salted butter if desired. 
  • Vanilla Greek Yogurt. Any yogurt variety works well. My top preferences are Greek and Icelandic yogurts for their thickness and creaminess. 
  • Maple Syrup. I’ve used honey in place of maple syrup with great results.
  • Eggs. You can use chia or “flax” eggs by combining 2 TBS ground chia seeds or flaxseed meal and 5 TBS warm water and letting it set for 10 minutes, then use in the recipe. The muffins might bake flatter if you do this. 
  • Whole wheat flour. All-purpose, spelt, whole wheat pastry flour, white whole wheat flour, etc. can be used in place of regular whole wheat flour.
  • Pumpkin Pie Spice. Use store bought or make your own with this recipe: 
Homemade Pumpkin Pie Spice
Use this recipe to make your own homemade pumpkin pie spice! 
Or, to make only 1 tablespoon of pumpkin pie spice combine: 
  • 1 ½ tsp cinnamon
  • ½ tsp nutmeg
  • ½ tsp cloves
  • ½ tsp allspice
Store
Store these healthy pumpkin muffins in an airtight container at room temperature for up to 3 days, or in the refrigerator for up to 1 week. 
Freeze
  1. Let muffins cool completely
  2. Transfer to an airtight container or freezer-friendly plastic bag.
  3. Transfer to the freezer and freeze for up to 2 months. 
Reheat
Reheat the healthy pumpkin muffins in one of three ways:
  1. Warm in the microwave for about 40 seconds per muffin. 
  2. Remove from the freezer and let them thaw to room temperature overnight.
  3. Warm in the oven preheated to 325 degrees F for about 5-10  minutes or until warmed through.

Nutrition

Serving: 1muffin | Calories: 150kcal | Carbohydrates: 24g | Protein: 4g | Fat: 5g | Saturated Fat: 3g | Cholesterol: 38mg | Sodium: 199mg | Potassium: 187mg | Fiber: 2g | Sugar: 10g | Vitamin A: 3335IU | Vitamin C: 1mg | Calcium: 55mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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Recipe Rating




12 Comments

  1. 5 stars
    Made these yummies for the first time, and they were very good. Put in some flaxseed meal and used some pumpkin yogurt, and they were awesome.

  2. 5 stars
    Made these today. Love them! Full of flavor and super moist! And they are healthier! All the recipes look so good, I know I will be coming back here when I am looking for one.

  3. 5 stars
    These are very good and I made them as stated. I used salted butter, real eggs, King Arthur Measure for Measure gluten free flour, canned pumpkin and made the pumpkin pie spice mix. I added raisins and chopped walnuts also.
    The spice ratio is outstanding. It made 12 muffins.

  4. 5 stars
    Wow amazing! I made it dairy free with an overripe banana and added a little unsweetened applesauce. I used a cashewmilk vanilla yogurt made by forager instead of greek yogurt. It’s not too pumpkin flavored it was great! I made tiny muffins to try out my new muffin tin and they were done in about 16-17 minutes. Thank you!

  5. 5 stars
    Tried this recipe………Very tasty muffins……Kids loved them ……….Even with whole wheat flour, they were quite good