Cream Cheese Filled Pumpkin Muffins
These cream cheese-filled pumpkin muffins are one of my favorite ways to use my recipe on how to make pumpkin puree from fresh pumpkin and my easy sourdough starter recipe. I’ve been making them for years, especially in the fall when we harvest sugar pie pumpkins from the garden. They are also a favorite during calving season in the spring when I make a big batch to take to the barn for overnight snacks. Each muffin is soft and moist with warm pumpkin spice, a sweet cream cheese center, and a crunchy cinnamon crumble topping. The batter can even be mixed up ahead of time for a long sourdough fermentation, making these pumpkin muffins a delicious from-scratch breakfast or snack.
Quick Look: Cream Cheese Filled Pumpkin Muffins
- ⏱️ Prep Time: 15 minutes
- 🍳 Cook Time: 25 minutes
- 🕒 Total Time: 40 minutes
- 👥 Servings: 24
- 📊 Calories: ~217 kcal per serving (based on nutrition panel)
- 🔥 Cook Method: Oven-baked in muffin tin
- 👩🍳 Flavor Profile: Sweet and slightly tangy with warm pumpkin spice, moist crumb, and rich, creamy cream cheese filling.
- ⭐ Difficulty: Easy – beginner-friendly, simple mixing, filling, and baking.
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Why You'll Love This Recipe
- Freezer friendly: Make a big batch and freeze some for an easy breakfast or snack later.
- Full of fall flavor: Pumpkin, warm pumpkin pie spices, sweet cream cheese filling, and a crunchy cinnamon crumble make these muffins taste like fall in every bite.
- A great way to use sourdough discard: This recipe turns extra sourdough discard into something delicious instead of letting it go to waste. My homemade strawberry muffins and overnight sourdough pancakes are also great ways to use discard.
- Made with homemade pumpkin: If you have garden pumpkins on hand, homemade pumpkin puree works beautifully in these muffins as well as in my recipe on How To Make Pumpkin Pancakes.
- Make them ahead: The batter can be mixed up several hours ahead or the night before, making it easy to have fresh muffins ready for breakfast.
- Soft and moist: Pumpkin and sourdough help give these muffins a tender, moist texture without making them heavy.
- Creamy surprise in the middle: The sweet cream cheese filling takes these muffins from an everyday snack to something special. I love to make this by straining my Easy Yogurt Recipe for 12-24 hours until it's nice and thick.
- Great for breakfast or dessert: Serve them with fruit and yogurt for breakfast, pack them for a snack, or enjoy one as a simple fall dessert. These are delicious with a spread of my recipe on how to make butter from raw milk
Ingredients
- Salt – redmond salt is the healthiest because it contains a lot of natural minerals. Salt actually brings out the sweet rich flavor in baked goods.
For a full list of ingredients needed to make this recipe, see the recipe card below.
This post contains affiliate links, which means I make a small commission at no extra cost to you. See my full disclosure here.
How To Making Cream Cheese Filled Pumpkin Muffins
Step 1: Prepare the cream cheese filling. Mix the cream cheese and powdered sugar until smooth. Place on plastic wrap, roll into a 1½-inch log, seal the ends, and freeze for at least 2 hours.
Step 2: Mix the muffin batter. Combine the pumpkin, sourdough discard, oil or applesauce, sugar, and eggs. Add the flour, salt, baking soda, and spices, and mix just until combined.
Step 3: Ferment the batter. Take the cream cheese filling out of the freezer and set it aside to soften slightly. For a long-fermented sourdough muffin, cover the batter and leave it at room temperature for up to 12 hours or overnight. If baking right away, preheat the oven to 350°F.
Step 4: Fill the muffin cups. Grease a 24-cup muffin tin or use paper liners. Add a small amount of batter to each cup. Slice the cream cheese log into 24 pieces and place one piece in each muffin cup. Cover with the remaining batter.
Step 5: Add the topping and bake. Mix the topping ingredients and sprinkle over each muffin. Bake at 350°F for 20–25 minutes, or until lightly golden and a toothpick inserted into the muffin comes out clean. Don't overbake.
Step 6: Cool and store. Allow the muffins to cool completely on a wire rack before storing them in an airtight container in the refrigerator. Enjoy within 3–5 days or freeze for later.
Tips for Making Cream Cheese Filled Pumpkin Muffins
- Use thick pumpkin puree: If your homemade pumpkin puree is watery, drain off some of the excess liquid first so the muffins don't become too wet.
- Don't skip chilling the cream cheese: Freezing the cream cheese mixture makes it much easier to slice and keeps the filling in the center of the muffins while they bake.
- Don't overmix the batter: Mix just until the flour is incorporated. Overmixing can make the muffins dense instead of soft and tender.
- Give the batter room to ferment: If you're making these as long-fermented sourdough muffins, allow the batter to sit at room temperature for up to 12 hours or overnight before adding the cream cheese and baking.
- Don't overfill the muffin cups: Leave enough room for the muffins to rise without spilling over the sides.
- Cover the cream cheese completely: Make sure the cream cheese filling is surrounded by batter so it stays in the center as the muffins bake.
- Watch the baking time: Pumpkin muffins can become dry if overbaked. Remove them when they're lightly golden and a toothpick inserted into the muffin portion comes out clean.
- Cool before storing: Let the muffins cool completely before placing them in an airtight container and refrigerating because of the cream cheese filling.
- Freeze extras: These muffins freeze well, making them a convenient breakfast or fall snack to have on hand.
Cream Cheese Filled Pumpkin Muffins FAQs
Full-fat, brick-style cream cheese works best for the filling. Avoid whipped or spreadable cream cheese because it is softer and can be more difficult to work with. Let the cream cheese soften enough to mix easily with the powdered sugar, then freeze the filling in a log before adding it to the muffins.
Freezing the cream cheese filling before adding it to the muffins helps keep it in the center while baking. Be sure to add a layer of batter to the bottom of each muffin cup, place the chilled cream cheese in the center, and completely cover it with the remaining batter.
Because of the cream cheese filling, store the baked muffins in an airtight container in the refrigerator. They are best eaten within 3–5 days.
Yes! These pumpkin muffins freeze well. Once they have cooled completely, place them in an airtight freezer-safe container or wrap them individually before freezing. Allow them to thaw at room temperature for a few hours before serving.
Yes. The muffin batter can be mixed several hours ahead and left at room temperature for up to 12 hours or overnight for a longer sourdough fermentation. Prepare the cream cheese filling separately and keep it frozen until you're ready to assemble and bake the muffins.
Absolutely. Homemade pumpkin puree works great in these muffins. If your puree is particularly watery, drain off some of the excess moisture before using it so the muffin batter doesn't become too wet.
Yes. Active sourdough starter can be used in place of sourdough discard. Since this recipe is designed to use discard, there's no need to feed your starter specifically for this recipe.
Other Pumpkin Recipes Like This
If you try this recipe and love it, please come back and give it 5 stars! Tag me on Instagram @wagonwheelhomestead21. I can’t wait to see what all you make!
Cream Cheese Filled Pumpkin Muffins
Equipment
- 1 Stand mixer or a large mixing bowl Get an extra $20 off a bosch mixer when ordering from nutrimill.com/wagonwheel.
- 1 Cookie Paddles If you have a Bosch mixer, I recommend the cookie paddles with the metal top and the cake paddles. If you don't have a stand mixer, use a hand mixer or wooden spoon in a large bowl.
- 1 Muffin tin
- 1 Muffin liners
- 1 Plastic wrap
- 1 Ice Cream Scoop
- 1 measuring cups and spoons
Ingredients
Cream Cheese Filling:
- 8 oz cream cheese
- 1 cup powdered sugar
Muffin Batter:
- 4 large eggs
- 2 cups sugar
- 2 cups pumpkin puree
- 1 cup melted fat - butter, beef tallow or oil (can also use applesauce as an oil replacement)
- 3 cups flour
- 1 teaspoon cinnamon
- 1 teaspoon nutmeg
- 1 tsp cloves
- 1 ½ Tbl pumpkin pie spice
- 1 teaspoon salt
- 1 teaspoon baking soda
- 1 cup sourdough discard
Crumble Topping:
- ½ cup sugar
- ¼ cup flour
- 1 ½ teaspoon cinnamon
- 4 Tbl cold butter
Instructions
- A few hours before you want to bake these muffins, combine the cream cheese and powdered sugar in a small bowl. Mix with a hand held mixer to fully incorporate the sugar into the cream cheese.
- Place the cream cheese mixture into a piece of plastic wrap that is at least 12 inches long.
- Carefully roll the plastic wrap up around the cream cheese and shape it into a log that is about 1 ½ inches in diameter, closing the ends as much as possible.
- Place in the freezer to chill for at least 2 hours
- If you plan to bake the muffins right away, preheat your oven to 350 degrees.
- Grease muffin cups well or add paper liners to a 24 cup muffin tin.
- In the bowl of your stand mixer, mix together all the wet ingredients. Pumpkin, sourdough discard, oil or applesauce, sugar and eggs.
- Then add all the dry ingredients. Flour, salt, baking soda & spices. Mix just until combined.
- *If you want this recipe to have long fermented digestive and health benefits, you can leave it out on the counter for up to twelve hours or overnight.
To assemble muffins
- Use an ice cream scoop to spoon a small amount of batter into each muffin cup (just enough to cover the bottom of each cup, usually a couple Tablespoons).
- Slice the chilled log of cream cheese filling into 24 equal pieces and place a slice of the cream cheese mixture into each muffin cup.
- Divide the remaining batter among the muffin cups, carefully covering the cream cheese.
- Mix up the topping ingredients and sprinkle a small amount of the mixture over each of the muffins.
- Bake in your preheated oven for 20-25 minutes or until a toothpick inserted in the center of the muffins comes out clean. They will be a light golden brown. Don’t overbake.
- For best results, allow to cool completely on a wire rack before storing in an airtight container in the refrigerator.
- Best if eaten within 3-5 days, or store in the freezer for an easy breakfast or dessert later on.
Notes
- Long ferment: Mix the batter the night before and leave at room temperature overnight for easier digestion and a fresh breakfast in the morning.
- Pumpkin puree: Roast a whole pumpkin at 400°F for about 45 minutes, cool, remove the skin and seeds, and blend the flesh into puree. Refrigerate up to 1 week or freeze up to 3 months.
- Sourdough: Use sourdough discard or active starter.
- Fat: Use oil, melted butter, beef tallow, or coconut oil. For an oil-free option, use applesauce.
- Cream cheese: Homemade cream cheese works wonderfully in this recipe.
- Muffin liners: Paper liners make these muffins easy to grab and eat on the go.
- Mini muffins: Bake in a mini muffin pan for a kid-friendly snack.
- Variations: Add chocolate chips to the batter for an extra special treat.
These look so good!
I do not see the sourdough discard listed in the ingredients list. Can you please specify the quantity? Thanks much.
Oh dear, thanks for catching that. It's 1 cup 🙂
Hey thanks.😊. Can’t wait to try.
You're welcome!