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Healthy Pumpkin Cream Cheese Muffins


Our healthy pumpkin cream cheese muffins bring a flavor favorite to those who love the Starbucks muffins but want a healthier version.

Our easy recipe quickly creates the spiced pumpkin muffins with a creamy filling, to satisfy your craving for those Starbucks fall muffins. But ours bake up guilt-free!




Pumpkin just shouts “Fall is Here!”


Combine it with cinnamon, nutmeg, and, ginger, and add a dollop of cream cheese for a taste reminiscent of Mom’s pumpkin pie.

My daughter brought one of Starbucks’ muffins home a few days ago for me. She sometimes surprises me with a small treat.  ( Aren’t kids wonderful! )

I thought about saving it for after dinner. And I did wait a few minutes. But that warm, spicy aroma called out. Yes, my muffin became my appetizer that day.

Guilty as charged! I justified it with the knowledge that the pumpkin is a squash. Therefore, my muffin might fall into the vegetable category. Yes, I know, it was quite a leap. But the muffin tasted good, anyway.

However, that made me think. Why not create a healthier version of those autumn wonders? Traditionally, muffins hardly qualify as healthy food. But by changing a few ingredients, perhaps these could become a little closer to healthy and still be delicious.


healthy pumpkin cream cheese muffins

Pumpkin Cream Cheese Muffins







These healthy copycat Starbucks pumpkin cream cheese muffins start with white whole wheat flour. You can substitute another flour if you prefer, but we like the nutrition of white whole wheat combined with the lighter taste and texture. Moreover, white whole wheat flour boosts your fiber level, just like its cousin, whole wheat flour from red wheat.

For the pumpkin, choose either fresh pumpkin puree or the more convenient, canned pumpkin puree. Be careful to not grab the pumpkin pie filling which is next to the pumpkin puree in most groceries. That contains refined sugars and sometimes other ingredients that we want to avoid.

I addition, Stevia is a plant-based, no-calorie sweetener that’s clean eating friendly, and it’s highly concentrated. You just need 1 ½ teaspoon for the muffin batter! Find it at your local grocery, or online here.

Need more reason to try these delicious muffins?



healthy pumpkin cream cheese muffins | squash

Photo by Rob Fallows from FreeImages

Pumpkin Fun Facts

  • Pumpkins belong to the winter squash family, Cucurbitaceae. (Pumpkins are Cucurbita pepo)
  • Although we call them vegetables, science considers them a fruit. Here’s why.
  • But, this fruit aligns more closely with vegetables in nutritional analysis.
  • Pumpkins are native to North America.
  • These nutritional powerhouses contain about 245% RDA of Vitamin A per cup.
  • They also contain lutein and zeaxanthin, which help promote eye health.
  • Other important nutrients include fiber, vitamin C, potassium, copper, manganese, vitamin B2, Vitamin E, and Iron.
  • Pumpkins contain high amounts of antioxidants, which studies show help fight diseases including cancer.
  • This versatile food finds its way into many foods, including custards, pies, pancakes, cookies, roasted vegetables, and soups. You might even find it in pasta or pasta sauce.
  • Pumpkin seeds are healthy, too! If you puree your own to use, save the seeds. Snack on them raw or roasted. Or toss a few in your salad. Studies reveal they may help bladder and heart health.


healthy pumpkin cream cheese muffins

Pumpkin Cream Cheese Muffins

Pumpkin, spice, and cream cheese make these delicious pumpkin cream cheese muffins are a healthier version of the fall Starbucks favorite.
Prep Time 15 minutes
Cook Time 20 minutes
cooling time 10 minutes
Total Time 45 minutes
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 131 kcal



  • cup plain nonfat Greek yogurt
  • ½ cup cream cheese softened
  • ½ tsp liquid stevia or 1/2 cup allulose, to taste
  • 1 tsp vanilla extract


  • 2 cups white whole wheat flour or whole wheat flour
  • ½ tsp ground ginger
  • tbsp ground cinnamon
  • ½ tsp nutmeg
  • tsp baking powder
  • ½ tsp baking soda
  • ½ tsp salt
  • 1 tbsp unsalted butter or coconut oil, melted
  • 2 large egg whites at room temperature
  • tsp liquid stevia
  • ¼ cup plain nonfat Greek yogurt or substitute block style cream cheese
  • 1 cup pumpkin puree at room temperature, not pumpkin pie filling
  • ½ cup nonfat milk oat milk substitutes well here. Or use other plant-based milk


Preheat oven to 350°F. Line 12 muffin cups with paper or silicone liners and spray lightly with a nonstick cooking spray.

    Prepare the filling.

    • Beat the yogurt and cream cheese with a mixer until smooth and creamy.
    • Add the stevia and vanilla. Beat until fully mixed. Set aside.

    Prepare the muffin batter.

    • In a medium bowl, whisk together the flour, ginger, cinnamon, nutmeg, baking powder, baking soda, and salt.
    • Using a separate bowl, whisk together the butter, egg white, stevia, and vanilla.
    • Add the yogurt. Mix until there are no remaining large lumps. Some small lumps may remain.
    • Stir in the pumpkin puree and stir to combine.
    • Add about ½ of the flour mixture to the egg mixture. Stir gently.
    • Stir in the milk to combine.
    • Add the remaining flour mixture and stir just until combined. Avoid over mixing.
    • Using about half the batter, spoon it evening between the 12 muffin cups.
    • Carefully spoon the filling mix into the center of each batter. Try to avoid any filling seeping to the side of the muffins.
    • Top with the remaining batter. It is ok if some of the filling shows through.
    • Bake at 350°F about 20-24 minutes. When done, the pumpkin portion will feel firm when touched. You may also test the pumpkin portion with a toothpick. It will come out clean when they are done.
    • Cool in the cups for 10 minutes before transferring to a cooling rack.½


    We found that the block-style cream cheese works better than the tub style. It provided a firmer filling.
    Use any type of cream cheese you prefer, including fat-free or regular.
    If you prefer a little less spice, just reduce the portions of cinnamon, nutmeg, and ginger slightly. We developed this recipe for a full-flavored muffin, but some prefer less so.
    Filling: To omit stevia in filling, use 1/2 cup of granulated sugar. This gives a sweeter filling which some consider more natural.
    Batter: To omit stevia in the batter, use 1/2 to 3/4 cup of maple syrup or honey, depending on your sweetness preference. Omit the milk when making this replacement.
    Some prefer to pipe the filling into the muffins. To do this, simply divide all the batter between the 12 cups. Use a piping bag or a zip-style bag with a corner removed to pipe the filling into the center of each.
    Fancy Idea: Intentionally leaving a little of the filling showing out the top gives a snow-topped mountain look. You can even sprinkle some colored sugar over the filling when it is baked for a bit more decor.
    Prefer larger muffins? This recipe easily converts to the mammoth-sized muffins we find in some restaurants. You may either double the recipe to create 12 jumbo muffins or simply divide into 6 muffin cups for 6 jumbos. Baking time will need to be extended accordingly.


    Calories: 131kcalCarbohydrates: 18gProtein: 5gFat: 5gSaturated Fat: 3gCholesterol: 14mgSodium: 259mgPotassium: 120mgFiber: 3gSugar: 2gVitamin A: 3355IUVitamin C: 1mgCalcium: 95mgIron: 1mg
    Keyword cinnamon, cream cheese, muffin, pumpkin, spice
    Tried this recipe?Let us know how it was!



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