These pumpkin cream cheese muffins are everything I crave when fall sets in—warm spices, tender pumpkin cake, a creamy cheesecake center, and a sweet crumbly topping that makes every bite feel like a celebration of the season. They’re soft, rich, and incredibly satisfying, perfect with a cup of hot coffee or tea.

Why You’ll Love This Recipe

I love how these muffins bring together the best elements of pumpkin spice season in one bite. They taste like a slice of pumpkin roll and a cheesecake had a baby. The texture is unbelievably soft and moist thanks to the pumpkin purée, while the cheesecake filling is subtly sweet and tangy. And that buttery crumb topping? It seals the deal. These muffins also stay fresh for days, making them ideal for breakfast, snack time, or dessert.

Ingredients

(Here’s a tip: Check out the full list of ingredients and measurements in the recipe card below.)

Crumb Topping

• 1/3 cup packed light or dark brown sugar

• 1 teaspoon ground cinnamon

• 1/4 cup (4 tablespoons) unsalted butter, melted

• 2/3 cup all-purpose flour

Pumpkin Muffins

• 1 and 3/4 cups all-purpose flour

• 1 teaspoon baking powder

• 1 teaspoon baking soda

• 1/2 teaspoon salt

• 2 teaspoons ground cinnamon

• 1 teaspoon pumpkin pie spice

• 1/2 cup packed light or dark brown sugar

• 1/2 cup granulated sugar

• 2 large eggs, at room temperature

• 1 cup canned pumpkin purée

• 1/2 cup vegetable oil (or melted coconut oil)

• 1/3 cup milk

• 1 teaspoon pure vanilla extract

Cream Cheese Filling

• 6 ounces full-fat brick cream cheese, softened

• 1 egg yolk, at room temperature

• 1/2 teaspoon pure vanilla extract

• 3 tablespoons granulated sugar

Directions

1. I start by preheating the oven to 425°F (218°C) and lining a 12-count muffin pan with paper liners or spraying it with nonstick spray.

2. For the crumb topping, I mix brown sugar, cinnamon, and melted butter in a small bowl. Then I stir in the flour with a fork until crumbly—no overmixing!

3. In a large bowl, I whisk together the dry muffin ingredients: flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice.

4. In a separate medium bowl, I whisk the wet ingredients: brown sugar, granulated sugar, eggs, pumpkin, oil, milk, and vanilla. I pour this mixture into the dry ingredients and gently whisk until just combined.

5. To make the cream cheese filling, I beat the cream cheese until smooth, then mix in the egg yolk, vanilla, and sugar until creamy and combined.

6. I spoon a heaping tablespoon of muffin batter into each muffin cup, then add a spoonful of cheesecake filling on top, and finish with more muffin batter to fill each cup. A little cheesecake filling showing on top is totally fine!

7. I sprinkle the crumb topping over each muffin and gently press it down so it sticks.

8. I bake the muffins for 5 minutes at 425°F, then lower the oven temperature to 350°F (177°C) and continue baking for another 15–17 minutes until a toothpick comes out clean.

9. I let the muffins cool in the pan for at least 10 minutes before digging in.

Servings and Timing

This recipe yields about 12 to 14 muffins.
Prep Time: 25 minutes
Cook Time: 22 minutes
Total Time: 50 minutes

Variations

• Mini Muffins: I make them mini by reducing the baking time to 10–12 minutes total—perfect for parties or snack trays.

• Loaf Version: I’ve baked this batter in a standard loaf pan before. I reduce the cream cheese filling slightly and bake it for 50–60 minutes.

• Nutty Crunch: I sometimes add chopped pecans or walnuts to the crumb topping for extra texture.

• Chocolate Chips: For a sweeter twist, I toss in mini chocolate chips into the pumpkin batter.

Storage/Reheating

Once cooled, I store these muffins in an airtight container:

• At room temperature: for up to 2 days

• In the refrigerator: for up to 1 week

For longer storage, I freeze them for up to 3 months. When ready to enjoy, I thaw them overnight in the fridge and warm them in the microwave for about 15–20 seconds.

FAQs

What kind of pumpkin should I use?

I always use canned pumpkin purée, not pumpkin pie filling. The texture and flavor are perfect for baking.

Can I skip the cream cheese filling?

Absolutely. If I’m in a rush or just want a simpler muffin, I leave out the cream cheese and still get an amazing pumpkin muffin.

How do I make these muffins more moist?

They’re already super moist thanks to the pumpkin and oil, but using full-fat dairy and not overbaking them keeps them extra tender.

Can I make these gluten-free?

Yes, I substitute a 1:1 gluten-free baking flour and it works well. I make sure it’s a blend designed for baking.

How do I know when the muffins are done?

I insert a toothpick into the muffin part (not the cheesecake) and look for moist crumbs, not raw batter. The tops should also spring back slightly when touched.

Conclusion

These pumpkin cream cheese muffins are everything I love about fall wrapped into one cozy treat. The spiced pumpkin base, rich cream cheese center, and crumbly sweet topping make them irresistible. Whether I’m baking for a weekend brunch, a school snack, or just to satisfy my seasonal cravings, this recipe never lets me down. I hope it becomes a favorite in your kitchen too.