Healthy Pumpkin Muffins

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The Best Healthy Pumpkin Muffin recipe is easy to make, yielding moist, tender muffins with a pumpkin spice kiss.

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It’s that time of year again. Time to start thinking about pumpkin spice, fall festivities, and cozy sweaters. But what do you eat?

Pumpkin muffins are the perfect recipe for this season in all its glory! You can enjoy these healthy muffins at breakfast, lunch, dinner, or dessert (or a snack!) without having to worry too much about calories or carbs because they’re made with whole grains instead of white flour. So go ahead and indulge your sweet tooth without worrying too much-these will make it easier on your waistline.

In this blog post, I will show you how to make healthy pumpkin muffins that taste just as good as nutritious!

I do not participate in the pumpkin pie spice craze, but this is my first year participating.

My inspiration for these muffins was a pumpkin latte. I figured it would be fun to create a pumpkin muffin that incorporated a breakfast in one bite.

Let’s talk about how to make healthy pumpkin muffins.

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Key Ingredients:

To make these fantastic healthy pumpkin muffins, you will need the following key ingredients: 

Whole Wheat Flour

Getting more fiber in your diet is one way to improve health, and using whole wheat flour is key.

Unbleached All-Purpose Flour

You never want to use 100% of whole wheat flour because of the final texture. Adding some all-purpose flour gives us the desired muffin.

Pumpkin Pie Spice

The fantastic combination of warm spices of ginger, nutmeg, and allspice does wonders for this recipe.

Light Brown Sugar

Imperial sugar makes some of the best sugar on the market. Imperial Sugar is one of the largest processors and marketers of refined sugar in the U.S. supplying high-quality products to food manufacturers, retail grocers and foodservice distributors.

Canned Pumpkin Puree

Make sure you do not buy pumpkin pie mix. That will get you the wrong results. 


What’s a latte without the milk. I use cashew milk because it has the least number of calories out of the alternative milk.

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How To Make the Best Healthy Pumpkin Muffins

Having a healthy snack to enjoy is essential, especially around the holidays. Here’s what you’ll need to make these amazing pumpkin muffins.

Step 1: Preheat oven to 375°F. In a large mixing bowl, combine whole wheat and all-purpose flour, baking powder, pumpkin pie spice, and salt.

Step 2: In another bowl, whisk pumpkin puree, butter, olive oil, ¾ cup brown sugar, eggs, milk, and vanilla extract until smooth. Pour wet ingredients into the dry and blend until smooth, but some lumps are welcomed. Spray a 12-muffin tin with cooking spray, fill each 2/3 full. Sprinkle top with remaining brown sugar, bake for 15 minutes. Cool completely before enjoying!

Pumpkin Muffins Recipe Tips & Tricks:

Here are some of my top tips and tricks to help you make these delicious muffins: 

  • Using the muffin method is the best way to get tender muffins with the perfect crumb. 
  • Feel free to use cinnamon as a swap for the pumpkin spice.
  • You can add pecans, chocolate chips, raisins, or whatever else your imagination and taste buds can enjoy. 
  • Most healthy pumpkin muffins will use maple syrup or honey. The light brown sugar provides moisture and a lovely maple flavor.
  • You can use any muffin pan regardless if it’s a muffin tin or silicone muffin pan.

Frequently Asked Questions

Here are the answers to some of the most frequently asked questions about healthy pumpkin muffins:

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What are the health benefits of pumpkin?

Pumpkin is a superfood and contains many health benefits, including:
1) Antioxidants
2) High fiber content
3) Vitamin A, C & K. Vitamin A can help reduce the risk of cancer while also promoting healthy eyesight and skin. Vitamin C helps maintain healthy blood vessels as well as bones, teeth, cartilage, and gums. Vitamin K is essential for bone formation and repairing blood vessels which can help protect against heart disease, osteoporosis, stroke, and dementia.

What kind of pumpkin should you use to make healthy muffins?

Canned pumpkin is best but you can use any pumpkin. However, I recommend using sugar pie pumpkins or butternut squash. These varieties are sweeter than regular carving pumpkins and have less moisture, resulting in a more consistent texture for your healthy pumpkin muffin recipe. Also, it would help if you strained homemade pumpkin puree to remove excess water. Otherwise, you will end up with a soggy muffin!

What does “scooping” mean when it comes to measuring ingredients?

When baking, it is crucial to always measure your dry ingredients by scooping them into a cup with the measuring utensil and leveling off any excess. Scooping ensures that all of your wet and dry measurements will be accurate so that everything turns out as intended. If you pour your ingredients into your measuring cup, they will come out too heavy, and you risk over or under-baking your muffins.

Why do I use baking powder and not baking soda?

I noticed most healthy pumpkin muffin recipes are anti-baking powder. However, I’ve had this muffin recipe in my family for decades, and it’s never called for baking soda.

The rule of thumb is to use baking powder for leaving when no acidic ingredients are being added because it doesn’t need help to rise.

Use baking soda when an acidic ingredient (buttermilk, vinegar, or lemon juice) is used to help it rise.

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What can I add to the pumpkin muffin batter?

Many people like adding chocolate chips or raisins for some extra sweetness and texture. You can also use butternut squash in place of pumpkin puree if you prefer something less sweet. Some other ideas are to add shredded zucchini or chopped walnuts.

How long do pumpkin muffins last?

Pumpkin and other fruit-based baked goods are best if eaten within a week of making them. You can freeze these for up to 3 months without compromising the taste or texture too much. If you don’t think you will get to them within a week, it is best to freeze the muffins before baking. This way, they are not exposed to too much moisture in the freezer and won’t be ruined.

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How do I know if my muffins are done?

Insert a toothpick into the pumpkin muffin top, and if it comes out clean, with no batter stuck to the toothpick, your muffins are done. If you see wet batter on the pick when you pull it back out of the muffin, keep them in for another five minutes or so until they are finished baking.

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Can I use muffin liners?

Absolutely! It is best to use parchment paper or silicone liners in a muffin pan so that the batter does not stick when you remove them. This will help the pumpkin muffins come out cleanly and also keep their shape for presentation purposes. I chose not to use any because they come out of the muffin pan easily.

Common One to One Substitutions:

Don’t have everything you need? No worries. Here are some of the most common substitutions for this dish:

  • If you have a gluten allergy, swap the whole wheat and all-purpose flour for gluten-free flour.
  • Feel free to swap out the avocado oil for canola oil, olive oil, or coconut oil.
  • You can also swap out the light brown sugar for dark brown sugar if needed.
  • Feel free to use any milk of choice, almond milk, coconut milk, 2% milk, or whole milk.
  • Use Imperial Sugars Steviacane® (Stevia + sugar blend) for an even healthier muffin.
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Can I make it ahead?


If you want to make this dish ahead of time, here’s how to do it:

Healthy Pumpkin Muffins – The muffins can be prepared a day in advance and stored in the fridge in an airtight container for 7 days. It will also keep in the freezer for up to 3 months. If frozen, let it thaw in the fridge for 24 hours before using it. Reheat in a 300°F oven for 5 minutes or zap in the microwave for 30-60 seconds.

What to Serve with Healthy Pumpkin Muffins?

The options are wide open when it comes to pairing these mouthwatering pumpkin muffins with aside. It all depends on the time of day you eat. Here are a few options:

More Fall Recipe Ideas:

After you finish making and enjoying these incredible pumpkin muffins, please leave me a 5-star review below and comment on Instagram so that others can see how tasty your meal was tonight!!

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Healthy Pumpkin Muffins

Kenneth Temple
The Best Healthy Pumpkin Muffin recipe is easy to make, yielding moist, tender muffins with a pumpkin spice kiss.
5 from 1 vote
Prep Time 10 mins
Cook Time 15 mins
Cool 5 mins
Total Time 30 mins
Course Breakfast, Side Dish, Snack
Cuisine American
Servings 12 persons
Calories 156 kcal


  • 1 ½ cup whole wheat flour 176g
  • ½ cup unbleached all-purpose flour 62g
  • 2 teaspoons baking powder 7g
  • 1 tablespoon pumpkin spice 4g
  • ½ teaspoon kosher salt 3g
  • 1 cup pumpkin puree 235g
  • 2 tablespoons melted unsalted butter
  • 2 tablespoons avocado oil
  • ¼ cup plus 2 teaspoons Imperial Sugar light brown sugar 72g
  • 2 large eggs slightly beaten
  • ½ cup cashew milk
  • 1 teaspoon vanilla extract
  • Cooking spray


  • Preheat oven to 375°F. In a large mixing bowl combine whole wheat and all- purpose flour, baking powder, pumpkin spice, and salt.
    Pumpkin Muffins Steps
  • In another bowl whisk pumpkin puree, butter, olive oil, ¾ cup brown sugar, eggs, milk and vanilla extract until smooth. Pour wet ingredients into the dry and blend until smooth but some lumps are welcomed. Spray a muffin pan with cooking spray, fill each up 2/3 full. In a small bowl combine remaining brown sugar and oats, sprinkle over top of muffins. Bake for 15 minutes. Cool for 5 minutes before enjoying!
    Pumpkin Muffins Steps1


You can add ½ cup dark chocolate chips to these muffins if you like.


Serving: 12gCalories: 156kcalCarbohydrates: 22.5gProtein: 3.8gFat: 5.5gSaturated Fat: 1.7gPolyunsaturated Fat: 0.4gMonounsaturated Fat: 2.2gTrans Fat: 0gCholesterol: 35.9mgSodium: 181.1mgPotassium: 14.3mgFiber: 2.5gSugar: 7.3gVitamin A: 43.2IUVitamin C: 0.06mgCalcium: 37.2mgIron: 4.3mg
Keyword fall muffins, healthy pumpkin muffins, muffins, muffins pumpkin, pumpkin muffins
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