Pumpkin Cream Cheese Muffins

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Pumpkin Cream Cheese Muffins are a copycat Starbucks treat. Packed with flavor, these muffins have a sweet cream cheese filling and spiced pumpkin seeds sprinkled on top. Easy to make and freezer friendly!

Make a batch of Pumpkin Cream Cold Brew to serve with these Starbucks inspired muffins. Total autumn heaven! Or try the new Apple Crisp Macchiato recipe to pair with these muffins.

Pumpkin muffins with cream cheese centers and spiced pepitas on top.
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Why this Muffin Recipe is Best

My friends know I love a Starbucks run from time to time. Especially when all the seasonal drinks and pastries start to come out in the fall.

What I love even more? Learning how to make my own versions of those tasty treats at home.

I’m always ready to invite a friend over to share a Mocha Latte or a plate of Cranberry Bliss Bars. And who can resist a slice of Starbucks Lemon Loaf?

After tasting one of the Starbucks pumpkin muffins filled with cream cheese last year, I knew I had to add them to my list of recipes to replicate.

If you love all things pumpkin (like me), I know you’ll fall in love with these muffins!

  • These taste just like Starbucks Pumpkin Cream Cheese Muffins but at a fraction of the cost.
  • The moist pumpkin muffins have a sweet cream cheese center baked right in.
  • A dusting of pumpkin spice and a few pumpkin seeds on top makes them look as amazing as they taste!

Be sure you try our delicious pumpkin bars and pumpkin roll next for more fall goodness!

Ingredient Notes

Ingredients needed for pumpkin cream cheese muffins.
  • Canned pumpkin. Make sure to use pure pumpkin puree–not pie filling–in today’s recipe.
  • Sugars. A combination of granulated sugar and brown sugar in the muffins creates a soft, yet moist texture.
  • Oil & Milk. Both are needed to add fat (which creates the delicious texture and flavor) without creating a dense muffin.
  • Vanilla extract. Use a pure vanilla extract or try our homemade vanilla extract recipe!
  • Pumpkin pie spice. Our Homemade Pumpkin Pie Spice is perfect here.
  • Cream cheese. Use full fat, unflavored cream cheese. Let it soften on the counter for a few minutes before making the filling.

Easy Instructions

Step by step photos showing how to make cream cheese filled pumpkin muffins.
  1. Make the Batter. To make pumpkin cream cheese muffins, start by mixing together the ingredients for the batter.
  2. Fill cupcake tins. Spoon the batter into prepared muffin tins. Then, beat together the cream cheese filling.
  3. Add cream cheese filling. To fill the muffins, add the filling to a ziploc bag. Snip of the corner and insert it into the center of each unbaked muffin. Pipe in the filling until you see a bit of it sticking out the top.
  4. Bake. Sprinkle pumpkin seeds and pumpkin spice over the muffins before baking.
Pumpkin Cream Cheese Muffins are a copycat Starbucks treat. Packed with flavor, these muffins have a sweet cream cheese filling and spiced pumpkin seeds sprinkled on top. Easy to make and freezer friendly!

Tips & Tricks

  • Be careful not to overmix the batter. After adding the dry ingredients, mix just until combined. Otherwise the muffins will be tough.
  • Use the back of a greased wooden spoon (or metal spoon) to make indentations in the top of each muffin before adding filling.
  • Toss the pumpkin seeds with the pie spice to get maximum pumpkin spice flavor!
  • The center of the muffins may look a little jiggly when these come out of the oven. That’s okay–the center will firm up as the muffins cool.
Pumpkin muffin with cream cheese filling cut in half.

Recipe FAQs

How do you store these muffins? How long do they keep?

You can store baked Pumpkin Cream Cheese Muffins in the refrigerator for up to 7 days.

Can I freeze these muffins with cream cheese filling?

Yes, these muffins hold up well to freezing! Double wrap in freezer bags to keep them fresh. They’ll keep well for up to 3 months. Let frozen pumpkin muffins thaw in the refrigerator overnight before serving.

Will the recipe work for mini muffins?

I haven’t tested this recipe in a mini muffin pan, but I expect it would work just fine. Small muffins will bake more quickly than regular sized muffins, so check on them frequently to avoid overcooking.

More Fall Recipes

Breakfast Muffin Recipes

See all Muffins recipes

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Pumpkin Cream Cheese Muffins

4.75 from 32 votes
By: Aimee
Pumpkin Cream Cheese Muffins are a copycat Starbucks treat. Packed with flavor, these muffins have a sweet cream cheese filling and spiced pumpkin seeds sprinkled on top. Easy to make and freezer friendly!
Prep Time: 20 minutes
Cook Time: 15 minutes
Total Time: 35 minutes
Servings: 14 muffins


For the Muffins

  • cup vegetable oil
  • 1 cup pure pumpkin puree no pumpkin pie filling
  • ½ cup granulated sugar
  • ½ cup light brown sugar packed
  • 2 large eggs
  • ¼ cup whole milk
  • 1 teaspoon vanilla extract
  • 2 cups all-purpose flour
  • 2 teaspoons pumpkin pie spice
  • ¼ teaspoon kosher salt
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder

For the Cream Cheese Filling

  • 1 package cream cheese, softened 8 oz
  • 1 Tablespoon all-purpose flour
  • ½ cup granulated sugar
  • 1 teaspoon vanilla extract
  • 1 teaspoon whole milk
  • ½ teaspoon kosher salt

For the Topping

  • ¼ cup pumpkin seeds
  • ½ teaspoon pumpkin pie spice
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  • Preheat oven to 375 degrees F. Line a muffin pan with paper liners and spray the liners with non-stick baking spray. Set aside.
  • In a large mixing bowl, combine the oil and pumpkin until blended. Add sugars and mix well.
  • Add in eggs, milk, and vanilla extract. Gently fold in the flour, pumpkin pie spice, salt, baking soda, and baking powder.
  • Spoon muffin batter into liners and fill about 3/4 full.
  • Using the back of a spoon, press the tops of each muffin until indented.
  • For the filling, beat cream cheese with flour, sugar, vanilla, milk, and salt until creamy, about 3-4 minutes. Spoon filling into a ziploc bag, and snip off the corner. Press the snipped end into the muffin batter and squeeze until it fills (you’ll want to see some on the top too).
  • Toss the pumpkin seeds with pumpkin pie spice. Sprinkle each muffin top with a few seeds.
  • Bake muffins for 15-20 minutes. They may be slightly jiggly until cooled.


  • Don’t overmix the muffin batter.
  • Spray the back of spoon with baking spray to create the hole in the muffin batter.
  • Store leftover muffins in airtight container in refrigerator for up to 7 days. Or freeze for up to 3 months.


Serving: 1muffin, Calories: 228kcal, Carbohydrates: 37g, Protein: 4g, Fat: 7g, Saturated Fat: 1g, Polyunsaturated Fat: 5g, Cholesterol: 29mg, Sodium: 221mg, Fiber: 1g, Sugar: 22g
Course: Muffins
Cuisine: American
Did you make this recipe?Mention @shugarysweets or tag #shugarysweets!

Welcome fall with these delicious Pumpkin Cream Cheese Muffins. Served with coffee, tea or a hot cup of cider, they’re a seasonal treat everyone will love.

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About Aimee

Aimee is a dessert lover (specifically rice krispie treats), workout enthusiast, self-taught foodie, and recipe creator.

Learn more about Aimee.

Affiliate Disclosure:**There may be affiliate links in this post! By clicking on them, or purchasing recommended items I may receive a small compensation. However, I only recommend products I love! Thank you for supporting Shugary Sweets! See my disclosure policy for more info**

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Posted on September 9, 2021

Comments & Reviews

  1. 5 stars
    10/10/23. I made these pumpkin muffins tonight and my family went crazy over them. I agree that the salt in the cream cheese is unnecessary but it wasn’t offensive. I doubled the spices and added cinnamon. I also added a tablespoon of vanilla pudding mix to the batter to ensure a moist crumb. They were delicious! Recipes’ a win for sure.

  2. Adding salt to the cream cheese was overwhelming and unnecessary. I added more sugar to cancel the saltiness. Also the muffins could use a little more sugar, I’d recommend 1/4 a cup extra white sugar to muffin mixture. They were good to me but a bit bland (I don’t like really sweet foods so they’re good to me.)

  3. 5 stars
    So many times I make a recipe from the internet and it’s a complete disaster but this is a winning recipe! I followed it to the note and they came out PERFECT!

  4. 5 stars
    These are better than Starbucks for sure! They are heavenly!! I will be adding cream cheese in pumpkin muffins all the time now!

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