This post may contain affiliate links. Please read our disclosure policy.
To make these pumpkin cream cheese muffins, I took my popular pumpkin muffins along with the knowledge gained from incorporating a cream cheese layer into my triple berry cheesecake muffins, to create the ultimate fall muffin. Sweater weather, here we come!
You’ll love these Pumpkin Muffins with Cream Cheese Filling
I didn’t earn the title of “muffin expert” by chance—it’s the result of months of intense dedication, trial and error, and an unwavering commitment to creating the perfect muffin. I spent half a year fine-tuning muffin recipes for my Muffin Cookbook, but these aren’t your everyday muffins.
They’re the kind of big, bakery-style muffins that you dream about—golden, towering, with that perfect crumb and flavor. And the best part? You don’t need fancy equipment or professional ovens; you can make these show-stopping muffins at home using a regular-sized muffin pan.
What sets my method apart isn’t just the recipes themselves. It’s the meticulous care and precision that went into developing my 4 key tips—tips that consistently produce bakery-quality results.
Thousands of bakers have tested and trusted these tips, with overwhelming success. This isn’t just theory; it’s proven. When home bakers follow my guidance, they know they’ll get the same results every time—perfectly risen, tender muffins that rival any bakery.
That kind of consistency is why I’ve earned the trust of muffin enthusiasts across the globe and why I’m proud to carry the title of muffin expert. It’s expertise built on real-world results, and I’m honored to help home bakers achieve the same success.
A cream cheese pumpkin muffin makes a great snack, dessert, or even the perfect Fall breakfast. Keep reading to make the most amazing pumpkin cream cheese muffins and wow your friends and family!
What you’ll need for Pumpkin Muffins with Cream Cheese
Cream cheese-stuffed pumpkin muffins? Yes, please! These muffins are made with surprisingly simple ingredients. Get the full recipe with measurements and ingredients in the recipe card below. Here’s what you’ll need:
- All-purpose flour: Make it gluten-free by using a 1:1 gluten-free baking flour.
- Granulated sugar
- Baking powder
- Baking soda
- Salt
- Ground cinnamon
- Ground nutmeg
- Ground ginger
- Pure pumpkin puree: 100% pure pumpkin canned
- Eggs
- Vegetable oil
- Milk
Cream Cheese Layer
- Cream cheese: room temperature
- Egg yolk
- Granulated sugar
- Vanilla extract
How to Make Pumpkin Cream Cheese Muffins
These delicious pumpkin cream cheese muffins look like they came from a bakery, but you will be able to make them from home with success when you follow my easy step-by-step instructions below. Keep reading for the full recipe in the recipe card below. Here are the easy steps:
Cream Cheese Layer
- Mix and chill cream cheese layer. Place the cream cheese, egg yolk, sugar, and vanilla extract in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth. Place the bowl in the freezer while you prep the rest of the recipe. Chilling the filling will help keep it from melting into the muffins.
Muffins
- Mix dry ingredients. In a large bowl combine the flour, granulated sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger. Stir together and set aside.
- Mix wet ingredients. In a larger mixing bowl combine the pumpkin, eggs, vegetable oil, and milk. Stir to combine.
- Combine wet and dry ingredients. Gradually mix the dry ingredients into the wet ingredients, mixing just until combined. The batter will be very thick.
- Rest batter and prep oven. Cover the bowl with a towel and allow the batter to rest for 15 minutes. During this time, preheat the oven to 425ºF / 220ºC.
- Prep muffin pan. For bakery style muffins, line a 12 count muffin pan with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. For the photos, I used tulip muffin liners, you can find them on amazon. Tulip liners naturally produce a taller muffin so you don’t need to do the every other muffin method. If you’re using regular muffin liners, I recommend filling every other muffin well.
- Assemble muffins. Fill the muffin cups with 2 tablespoons of batter. Drop 1 tbsp of the cream cheese mixture into each muffin cup. Use a toothpick to swirl into the batter. Then add 6 tablespoons of batter, covering the cream cheese. Top each muffin with ½ tbsp of cream cheese, swirling with a toothpick. Sprinkle the tops of the muffins with sanding sugar.
- Bake and cool. While one pan is baking, refrigerate the remaining batter in the bowl. Place one pan in the center of the oven and bake for 7 minutes at 425ºF / 220ºC, then keep the muffins in the oven, turn the temperature down to 350ºF / 180ºC and bake for 18-21 minutes if using regular muffin liners / bake for 20-25 minutes if using tulip muffin liners or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan. Repeat with the remaining batter, bumping the temperature back up to 425ºF / 220ºC.
Pumpkin Cream Cheese Muffin Variations
If you love indulging in pumpkin recipes during Fall season, or any time of year, you are going to be hooked on these muffins! Here are some swaps if you need or want to change the recipe:
- Gluten-free Pumpkin Cream Cheese Muffins: I’ve made these muffins with both regular all-purpose flour and gluten free flour with awesome results on multiple occasions. I recommend King Arthur’s Gluten Free Measure for Measure Flour. Use it as a one for one substitute for regular flour.
- Skip the cream cheese layer: If you just want pumpkin muffins without the cream cheese, use my pumpkin muffins recipe.
- Vegan Pumpkin Cream Cheese Muffins: Substitute dairy cream cheese with a plant-based cream cheese alternative and use flax eggs (ground flaxseed + water) in place of eggs. I have not tested this so I can’t attest to how this turns out.
- Pumpkin Cream Cheese Streusel Muffins: Top the muffins with a buttery crumb topping.
- Add nuts: Add chopped nuts (like pecans or walnuts) to the batter or as a topping for added crunch and texture.
- Chocolate Chip Pumpkin Cream Cheese Muffins: Fold in some chocolate chips to the muffin batter or the cream cheese filling for a sweeter, more indulgent muffin.
Serving Pumpkin Cream Cheese Swirl Muffins
Another great thing about these muffins is that they are great warm, cold and room temperature. You just can’t go wrong!
You can serve these with a cup of coffee, tea, hot chocolate or to really go all out on the Fall theme, a cup of warm apple cider.
How to store Cream Cheese Pumpkin Muffins
Storing and Freezing Muffins
Muffin Storage
If you’ll be eating the muffins within 24 hours of baking, you can leave them uncovered on the counter. The muffins will not dry out while left at room temperature for 1 day.
In fact, muffins are so moist they can become soggy and those crunchy, sugary tops can disappear when stored in an airtight container.
But I have a trick to help that – paper towels.
For longer storage, 2-4 days, line the bottom of an airtight container with paper towels. Place the muffins in a single layer in the container then cover the muffins with any additional layer of paper towels. The paper towels will act like a sponge, absorbing the moisture they release while they are stored.
If the paper towels become too moist around day 2 or day 3, replace them with fresh paper towels.
How To Freeze Muffins
Individually wrap each muffin in plastic wrap. Then place them in a ziploc bag or airtight container and place in the freezer for up to 3 months.
To thaw, leave them at room temperature until defrosted, about 1 hour. Or unwrap them and microwave at 20 second intervals until defrosted.
More Pumpkin Recipes
Tap stars to rate!
Pumpkin Cream Cheese Muffin Recipe
Ingredients
- 3 cups (360 grams) all-purpose flour
- 1 ¾ cups (350 grams) granulated sugar
- 3 tsp baking powder
- ½ tsp baking soda
- 1 tsp salt
- 3 tsp ground cinnamon
- ¼ tsp ground nutmeg
- ¼ tsp ground ginger
- 1 15 oz can (425 grams) 100% pure pumpkin puree
- 2 large eggs
- ¾ cup (117 ml) vegetable oil
- ½ cup (118 ml) milk
Cream Cheese Layer
- 8 oz (227 grams) cream cheese, room temperature
- 1 egg yolk
- ½ cup (100 grams) granulated sugar
- 2 tsp vanilla extract
Instructions
Cream Cheese Layer
- Place the cream cheese, egg yolk, sugar, and vanilla extract in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth. Place the bowl in the freezer while you prep the rest of the recipe. Chilling the filling will help keep it from melting into the muffins.
Muffins
- In a mixing bowl combine the flour, granulated sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger. Stir together and set aside.
- In a larger mixing bowl combine the pumpkin, eggs, vegetable oil, and milk. Stir to combine.
- Gradually mix the dry ingredients into the wet ingredients, mixing just until combined. The batter will be very thick.
- Cover the bowl with a towel and allow the batter to rest for 15 minutes. During this time, preheat the oven to 425ºF / 220ºC.
- For bakery style muffins, line a 12 count muffin pan with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. For the photos, I used tulip muffin liners, you can find them on amazon. Tulip liners naturally produce a taller muffin so you don’t need to do the every other muffin method. If you’re using regular muffin liners, I recommend filling every other muffin well.
- Fill the liners with 2 tablespoons of batter. Drop 1 tbsp of the cream cheese mixture into each muffin cup. Use a toothpick to swirl into the batter. Then add 6 tablespoons of batter, covering the cream cheese. Top each muffin with ½ tbsp of cream cheese, swirling with a toothpick. Sprinkle the tops with sanding sugar.
- While one pan is baking, refrigerate the remaining batter in the bowl. Place one pan in the center of the oven and bake for 7 minutes at 425ºF / 220ºC, then keep the muffins in the oven, turn the temperature down to 350ºF / 180ºC and bake for 18-21 minutes if using regular muffin liners / bake for 20-25 minutes if using tulip muffin liners or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan. Repeat with the remaining batter, bumping the temperature back up to 425ºF / 220ºC.
