by Olena

Healthy Pumpkin Muffins

Olena's image
Olena Osipov
5 from 11 votes

Healthy Pumpkin Muffins with whole wheat or spelt flour, maple syrup, and a tad of cream cheese. Breakfast or a snack, these pumpkin muffins are easy, tasty, and warm with Fall spices.

Love the flavor of pumpkin and pumpkin spice? Then you’ll also enjoy this healthy pumpkin pie, pumpkin bars, pumpkin cake, or pumpkin brownies! Don’t let pumpkin season pass you by!

Healthy Pumpkin Muffins

Healthy Pumpkin Muffin Recipe

Healthy pumpkin muffins truly cheer me up while I’m mourning the end of summer.

This healthy pumpkin muffins recipe has a spot on amount of pumpkin, pumpkin pie spice and cream cheese. Delicious!

Just like Starbucks pumpkin cream cheese muffins but with 2 times less sugar and fat, 1.5 times less calories and carbs, and 3 times more fiber!

Even better, the addition of spelt flour adds extra nutrients but works amazingly with baked goods. It’s practically become like my new all-purpose flour. I’ve made chocolate bread, banana bread, cinnamon rolls, and even chocolate chip pumpkin bread with it (among others!)

Healthy Pumpkin Muffins with bite

Also with pumpkin spice muffins, even picky eaters won’t notice their healthy factor – whole wheat flour. Because pumpkin pie spice goes so well with hearty whole grains.

More nutrients, more fiber, more muffins you can eat.

Plus, want to try even more pumpkin recipes? How about almond flour pumpkin bread, pumpkin protein oat bars, or even something savory like one-pot taco pasta with pumpkin or parmesan pumpkin and spinach quinoa?

Ingredients You Will Need

  • Canned pumpkin puree – not pumpkin pie filling. You can use homemade puree as well.
  • Eggs
  • Any oil – I forgot to take a picture of it but I like to use avocado or melted coconut oil.
  • Maple syrup or honey
  • Whole wheat or spelt flour – I used spelt.
  • Pumpkin pie spice
  • Cream cheese and pepitas – optional for filling.

ingredients for healthy pumpkin muffins

What Is Pumpkin Pie Spice?

If you are not familiar with pumpkin pie spice, it is just a blend of cinnamon, nutmeg, ginger, cloves and sometimes allspice. I always make my own pumpkin pie spice mix because it is way cheaper, I never run out and it doesn’t contain sulphites.

Easy, simple and healthy.

How to Make Healthy Pumpkin Muffins

This healthy pumpkin muffins recipe is easy like any of my healthy muffins. One bowl.

  • First whisk the eggs. This step eliminates old fashioned way of mixing wet and dry ingredients separately. Then add pumpkin puree, maple syrup, oil, pumpkin pie spice, baking powder, baking soda and salt. Whisk well until you no longer see white balls of baking powder.
  • Also if using honey, it takes a bit more effort to combine with other ingredients. Make sure honey is liquid or warm up solid honey on the stove or in a microwave. Add flour and gently stir with spatula. I let flour sit and absorb liquids for a few seconds before stirring again.

Now you are ready to bake your muffins or add optional but or so good cream cheese filling.

how to make Healthy Pumpkin Muffinshow to make Healthy Pumpkin Muffins

  • Add cream cheese filling. Amount is completely up to you – I use about 1-2 tsp. Distribute batter evenly between 12 openings of a tin – I use regular ice cream scoop. Make a cavity with a back of a spoon, add 1 tsp or more of cream cheese and swirl it with a toothpick.
  • Bake pumpkin muffins for 20 minutes at 375 degrees F. Even if you insert toothpick and it comes out a bit wet, remove muffins from the oven. You don’t want to overbake pumpkin muffins.

Kids loved this addition to whole wheat pumpkin muffins. Kind of like cheesecake pumpkin muffins.

how to make Healthy Pumpkin Muffinshow to make Healthy Pumpkin Muffinshow to make Healthy Pumpkin Muffinshow to make Healthy Pumpkin Muffinshow to make Healthy Pumpkin Muffinshow to make Healthy Pumpkin Muffins

Optional Add Ins

There are so many things you can add to pumpkin muffins:

  • Chocolate chips
  • Chopped walnuts, pecans or other nuts
  • Pumpkin seeds
  • Dried cranberries or mango
  • Crystalized ginger
  • Coconut flakes
  • Cacao nibs

Healthy Pumpkin Muffins in a muffin tin

How to Store and Freeze Pumpkin Muffins

To store and prevent muffins from drying, place in a resealable bag or airtight container and store on a counter for 3 days. These healthy pumpkin muffins do not contain much oil and rely on pumpkin’s water content. You want to keep muffins sealed.

Freeze baked and cooled pumpkin muffins same day to ensure freshness. Freeze for up to 3 months. To thaw just remove muffins from the freezer and let defrost in a bag for a few hours or overnight.

Enjoy these copycat Starbucks but healthy pumpkin muffins at home without the guilt or a hefty bill.

Healthy Pumpkin Muffins topped with pumpkin seeds

More Healthy Muffin Recipes

Or check out my full collection of muffins and quick bread recipes!

Healthy Pumpkin Muffins

Healthy Pumpkin Muffins

Healthy Pumpkin Muffins with whole wheat or spelt flour, maple syrup and a tad of cream cheese. Breakfast or a snack, these pumpkin muffins are easy, tasty and warm with Fall spices.
5 from 11 votes
Print Save Rate
Course: Muffins
Cuisine: North American
Prep Time: 10 minutes
Cook Time: 20 minutes
Servings: 12 muffins
Calories: 201kcal
Author: Olena Osipov


  • 2 large eggs
  • 1 1/4 cups pumpkin puree not pumpkin pie filling
  • 3/4 cup maple syrup or honey
  • 3 tbsp oil I used avocado
  • 1 tbsp pumpkin pie spice
  • 2 tsp baking powder aluminum free
  • 1 tsp baking soda
  • 1/2 tsp salt
  • 2 cups whole wheat spelt flour
  • 12 tsp or more cream cheese optional
  • Pumpkin seeds for garnish (optional)


  • Preheat oven to 375 degrees F and spray muffin tin with cooking spray. Set aside.
  • In a large mixing bowl, whisk the eggs. Add pumpkin puree, maple syrup, oil, pumpkin pie spice, baking powder, baking soda and salt; whisk well to combine.
  • Add flour and gently mix until combined.
  • Distribute batter evenly between 12 openings of a tin (I used regular ice cream scoop).
  • Optional: Make a cavity with a back of a spoon, add 1 tsp or more cream cheese, swirl with a toothpick and sprinkle with pumpkin seeds.
  • Bake for 20 minutes. Even if toothpick inserted in the centre comes out with a bit of crumbs - take them out.
  • Let muffins cool for a few minutes and transfer to a cooling rack to cool off completely.

Store: To prevent muffins from drying, place in a resealable bag or airtight container and store on a counter for 3 days. Freeze for up to 3 months.


    Optional add-ins: Chocolate chips, chopped walnuts, pecans or other nuts, pumpkin seeds, dried cranberries or mango, crystalized ginger, coconut flakes, cacao nibs.


    Serving: 1muffin | Calories: 201kcal | Carbohydrates: 35g | Protein: 4g | Fat: 7g | Saturated Fat: 2g | Cholesterol: 33mg | Sodium: 312mg | Potassium: 156mg | Fiber: 3g | Sugar: 19g | Vitamin A: 4078IU | Vitamin C: 1mg | Calcium: 72mg | Iron: 1mg
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    olena osipov in the studio

    Hello and welcome to iFOODreal.

    My name is Olena Osipov. I'm a mom to 2 boys, a wife to Alex and we reside on magical Vancouver Island in British Columbia, Canada. This is our healthy family recipes blog. Originally from Ukraine, I grew up on real food. As an adult, I struggled with diets for years because none worked long-term. Now for over 10 years, I cook easy healthy meals for my family. I can help you with “What’s for dinner?” too.

    25 comments on “Healthy Pumpkin Muffins

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    1. Hi, I’m planning on making pumpkin muffins and love several of yours recipes. What is the difference (flavor, texture) in your “Pumpkin chocolate chip bread”(can be made as muffins) and these “Pumpkin muffins”?

    2. Happy fall!!! I’m so excited to try theSe healthy pumpkin muffins! Do you happen to have the weight (in grams) of flour used? I’ll be using fresh milled flour and the measurements are usually quite off. I googled a conversion but was just curious if you have it handy. Thanks!!

    3. 5 stars
      Hi Olena,

      I made the pumpkin muffins, Delicious!!!! The only thing I omitted was the cream cheese, since I didn’t have it on hand but added a handful of crushed mixed nuts. Great recipe. Thank you.

    4. 5 stars
      This recipe sounds great! Can I use reduced fat cream cheese? Do you think it will make a big difference?

    5. 5 stars
      This recipe has become a standby. I use our favorite squash that we grow in our garden, North Georgia Roaster. I made these muffins to give to neighbors at Christmas. One neighbor remarked that it was the best muffin she had ever eaten! Since then we practically always have a batch in the kitchen for breakfast or for a healthy snack. The addition of the cream cheese in the muffin is genius. Thank you so for this recipe. I will be making it always!

    6. 5 stars
      Been waiting for it to cool down outside before I starting baking with pumpkin again. Today was the day. This was a perfect start to the season!

    7. 5 stars
      These were delicious. Really moist and easy to make.They had a hint of sweetness without being too sweet. I ended up using half honey and half maple syrup and whole wheat flour and they turned out great. I made half with chocolate chips for the kids and half with cream cheese for myself. The kids ended up wanting to eat the cream cheese ones and loved them! I was sad that I ran out of pumpkin so I could make 2 more batches! Great job Olena!

    8. 5 stars
      Olena, these were so delicious. The only thing I did differently was use toasted walnuts rather than the Pumpkin seeds. I have been baking for awhile now to eat healthier and had no idea until this recipe that you don’t have to use any oil or butter in the batter. Thanks again for another great recipe I will make again shortly.

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