by Olena

Healthy Pumpkin Muffins

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Olena Osipov
5 from 12 votes

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Healthy Pumpkin Muffins are light and moist, made with whole wheat or spelt flour, a dollop of cream cheese and chock full of mouth-watering fall spices. Ready in 30 minutes, they are perfect for breakfast and will win a spot in your favorite healthy muffin recipes collection!

Can’t get enough of pumpkin spice flavor? 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 in muffin tin

The Best Healthy Pumpkin Muffins

Healthy pumpkin muffins recipe are a delicious way to cheer up while mourning the end of summer days yet at the same time welcoming busy days of fall.

Other seasonal recipes that help make this transition include turkey stuffed acorn squash, butternut squash soup and baking recipes with pumpkin spice including healthy pumpkin bread!

These muffins are a copycat of 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! That makes them perfect for healthy snacks.

I am beginning to have quite a knack for transforming favorite restaurant (or coffee shop) recipes into their healthier, budget-friendly versions- like sous vide egg bites, chicken alfredo or healthier chicken parmesan.

Healthy pumpkin muffins on baking rack with a bite taken out of one.

Ingredients for Copycat Starbucks Cream Cheese Muffins

  • Canned pumpkin puree: Not pumpkin pie filling. You can use homemade puree as well, although it is often a bit more watery.
  • Eggs: To add lift and binding in baked goods.
  • Any oil: A neutral oil such as avocado or melted coconut oil.
  • Maple syrup or honey: I like the seasonal touch that maple syrup adds, but honey can be used as well.
  • Pure vanilla extract: Used to enhance the flavors, use pure not imitation.
  • Whole wheat or spelt flour: I used spelt, but whole wheat pumpkin muffins, works just as good!

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

  • Pumpkin pie spice: For all the fall vibes! Make your own homemade pumpkin spice blend or purchase at your grocer in the spice/baking aisle. If you love fall baked good with warm spices, also try gingerbread and gingersnap cookies.
  • Cream cheese and pepitas: Optional for filling, but if you are craving Starbucks pumpkin cream cheese muffin, this will satisfy.

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.

Whole wheat flour, pumpkin puree, maple syrup, cream cheese, eggs, pumpkin spice.

Why This Pumpkin Spice Muffins Recipe Works?

  • 100 % regular whole wheat flour and no refined sugar: Healthified version of your favorite Starbucks pumpkin cream cheese muffin!
  • Wholesome ingredients: Including pure pumpkin puree which is an amazing source of fiber.
  • Easy to make: Basic ingredients and in one bowl – less mess, less stress!
  • Freezer friendly: Make a batch now and freeze a few later to enjoy while viewing fall colors or after visiting the pumpkin patch!
  • Pumpkin spice craving satisfied: Move over pumpkin spice latte, these healthy pumpkin muffins with warming spices hit the spot! 

Want to try even more pumpkin recipes? How about almond flour pumpkin bread, pumpkin protein oat bars, soft pumpkin cookies or even something savory like one-pot taco pasta with pumpkin or parmesan pumpkin and spinach quinoa? It’s time to embrace everything fall has to offer with autumn inspired seasonal recipes!

How to Make Healthy Pumpkin Cream Cheese Muffins

This healthy pumpkin muffins recipe is easy like any of my healthy muffins. One bowl because life, am I right?!

  • 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.
  • Add flour: Stir gently to combine. Don’t over mix! Then scoop batter into a prepared muffin pan. I like to use an ice cream scoop!

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.

  • Add cream cheese filling. Amount is completely up to you – I used 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 cream cheese muffins. Cool on wire rack.

Kids loved the cream cheese addition to whole wheat pumpkin muffins. Kind of like cheesecake pumpkin muffins.

Optional Add-In’s and Variations

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

  • Chocolate chips for additional decadence.
  • Chopped walnuts, pecans or other nuts to satisfy crunch.
  • Pumpkin seeds for enhancing the fall pumpkin vibes.
  • Dried cranberries, mango, chopped dates or mango for additional texture.
  • Crystalized ginger adds another sweet seasonal taste.
  • Coconut flakes either mixed in, sprinkled on top or a little of both!
  • Cacao nibs for their healthy benefits, plus they satisfy a chocolate craving.
  • Egg-Free: Use a flax egg or chia egg.
  • Frosting: Skip the cream cheese swirl and top with healthy cream cheese frosting!

All out of pumpkin spice blend? Simplify by using 1 tsp cinnamon and 1/4 tsp each of ginger, nutmeg, cloves and all spice. Alternately, if your spice drawer is bare, use 2-3 tsp of cinnamon (depending on your love of cinnamon!) and call it good.

Tips for Best Results

  • For best results when you measure flour: gently stir your flour using a large spoon then spoon the correct amount into the measuring cup. Level the top of the measuring cup with a knife. Repeat as needed.
  • Don’t over mix your muffin batter when adding your flour into your wet ingredients in the bowl. Over mixing will lead to dense, tough muffin results. Also, don’t be tempted to use your mixer for this recipe.
  • Don’t over bake the muffins – this could lead to a dry muffin or worse yet, if you used cream cheese, burnt cream cheese.


Are pumpkin muffins healthy?

It really depends on your definition of healthy – but I consider these a healthy version of a pumpkin spice muffin as they are full of wholesome ingredients, contain only non refined sugar and have minimal oil.

Is canned pumpkin the same as pumpkin puree?

Yes – just be sure not to use pumpkin pie filling as that contains additional spices and ingredients.

Can I make this into pumpkin bread instead of muffins?

I suppose you could, it will need to bake longer and you could just swirl the cream cheese at the top – be watchful of it in the oven as it bakes, you may need to cover the top so the cream cheese doesn’t burn OR you could just make healthy pumpkin bread recipe.

Can I use whole wheat pastry flour vs whole wheat flour?

I have not tested it with pastry flour and there is a difference between whole wheat flour (milled from red hard wheat) and whole wheat pastry flour (milled from white soft wheat). Baking is a science and I am hesitant to say it would turn out exactly the same, but you could try it as a 1:1 substitute for whole wheat. Be sure to leave a comment if you try it that way!

Is it okay to use reduced fat cream cheese?

Yes, you may want to add more than 1-2 tsp for taste reasons, but that should work.

How can I keep muffins from sticking to the muffin pan?

Lightly spray liners lightly with oil or use parchment muffin liners for easier muffin removal from the pan after baking.

Healthy Pumpkin Muffins in a muffin tin

Serving Recommendations

We love to enjoy these muffins as a healthy grab and go breakfast or snack with or without a small smear of butter.

Making Pumpkin Muffins in Advance

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 healthy muffin recipes 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 healthified ‘Starbucks’ pumpkin cream cheese muffins at home without the guilt or a hefty bill.

More Healthy Muffin Recipes

close up of pumpkin cream cheese muffin on baking rack.
Healthy Pumpkin Muffins

Healthy Pumpkin Muffins

Healthy Pumpkin Muffins are light and moist, made with whole wheat or spelt flour, a dollop of cream cheese and chock full of mouth-watering fall spices. Ready in 30 minutes, they are perfect for breakfast or an afternoon snack.
5 from 12 votes
Print Save Rate
Course: Muffins
Cuisine: North American
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 12 muffins
Calories: 201kcal
Author: Olena Osipov



  • 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: Freeze baked and cooled pumpkin muffins same day to ensure freshness. Freeze for up to 3 months.


      • Substitute pumpkin spice blend: Use 1 tsp cinnamon and 1/4 tsp each of ginger, nutmeg, cloves and all spice. Alternately, use 2-3 tsp of cinnamon if you are out of all other spices.
      • Reduced fat cream cheese: Can be used in place of regular cream cheese.
      • Flour substitutions: Baking is a science and this recipe cannot be used with other flours except wheat flour. That being said, some readers have had success with whole wheat pastry flour.
      • Egg free: Try flax egg or chia egg.
      • Muffins into quick bread: This is possible with a longer cooking time, you may need to cover the top loosely with foil near the end of baking time if you notice the top starts begins to brown, or cream cheese starts to burn. 
      See recipe post for more tips and FAQs.


      Serving: 1muffin | Calories: 201kcal | Carbohydrates: 35g | Protein: 4g | Fat: 7g | Saturated Fat: 2g | Cholesterol: 33mg | Sodium: 312mg | Fiber: 3g | Sugar: 19g

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      31 comments on “Healthy Pumpkin Muffins

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      1. If you don’t have aluminum free baking powder can you still use it in the Health Pumpkin Muffins (Starbucks Copycat)?

      2. 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”?

      3. 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!!

      4. 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.

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