Pumpkin Spice Cheesecake Mousse Muffins
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These pumpkin spice muffins have tall pecan crumble tops and a creamy cheesecake mousse center. I use tulip parchment liners for the big bakery look, then core and fill the muffins once they have cooled completely. The pumpkin and cheesecake together are such a wonderful combination.
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That cheesecake center was worth the time
I worked on this cheesecake flavor for so long, and it is such a dream with pumpkin. The miso paste and unfortified nutritional yeast are essential here. Those little amounts help give the mousse the cheesecake flavor I was looking for.
I love these as big muffins in tulip liners, with all that pecan crumble piled on top. The creamy filling goes in after baking, so you get the pumpkin muffin, crumble, and cheesecake center together.
Ingredient notes
Key ingredients
Pumpkin puree and warm spices
Pumpkin puree, cinnamon, cardamom, nutmeg, ginger, and pumpkin spice emulsion give the batter its pumpkin spice flavor. Use the listed puree rather than a sweetened pumpkin pie filling.
Plain unsweetened Greek-style yogurt
Use the Greek-style yogurt listed for the muffin batter, at room temperature. The mousse has its own smaller amount of plain unsweetened yogurt.
Pecans and cold butter
Work the crumble together until it holds when squeezed, then stir in the chopped pecans. Keep it chilled while you make the batter.
Miso paste and unfortified nutritional yeast
Please do not leave these out. They are essential to the cheesecake flavor I worked so long to get. Use mild white or yellow miso and sift the unfortified nutritional yeast.
Cream cheese and yogurt
Cream cheese and plain unsweetened yogurt make the creamy cheesecake center. Add the chilled mousse only after the muffins have cooled completely.
Make the muffins ahead, then fill them when you are ready
Bake the pumpkin muffins with their pecan crumble ahead of time. For freezer storage, leave them unfilled and add freshly made chilled cheesecake mousse after thawing.
| What to prepare | How far ahead | How to store | When you are ready |
|---|---|---|---|
| Pecan crumble | 1 day ahead | Cover and refrigerate. | Break into clusters and divide over the batter before baking. |
| Cheesecake mousse | 1 day ahead | Keep covered in the refrigerator at 40°F (4°C) or below. | Pipe into completely cooled muffins, keeping the mousse chilled. |
| Baked, unfilled muffins with crumble | Up to 2 months frozen | Cool completely, wrap individually, and protect the tops in a freezer container or bag. | Thaw overnight in the refrigerator while wrapped. Once fully thawed, core and fill with fresh chilled mousse. |
| Filled muffins | Up to 3 days refrigerated | Cover in an airtight container in the refrigerator. | Serve chilled and return leftovers to the refrigerator promptly. |
Freeze after baking and cooling
Leave the muffin centers intact until after thawing. Cool the baked muffins completely, keep their liners on, and wrap them individually. Protect the pecan crumble from being crushed and freeze for up to 2 months.
Thaw before coring and filling
Move the wrapped muffins to the refrigerator the night before you need them. Once fully thawed, unwrap, make the cavities, and pipe in freshly made chilled mousse. Keep the filled muffins refrigerated. Count any mousse storage before filling toward the three-day filled-muffin refrigerator window.
From this recipe
Tested notes
I use tall tulip parchment liners in standard muffin pans for 10 large muffins. Fill the batter to the level of the pan rim and divide all the crumble evenly among them. It will look tall, which is the look shown in the photos.
With regular liners, fill about three-quarters full with batter and add crumble up to the top of the liners. Expect about 15 regular muffins.
Line alternating cups so there is an empty cup between muffins. Begin checking large muffins at 22 minutes or regular muffins at 18 minutes, then use the center tester check to decide when they are finished.
For the dairy-free version, I highly recommend two small pinches of food-grade lactic acid powder in the mousse. A little goes a long way.
Cool the muffins completely before coring and filling. Keep the bottom intact so the mousse stays inside.
Testing notes
Why this works
Give the tops room
Line alternating muffin cups, leaving an empty cup between muffins so their tall tops have room to rise and spread.
Choose the liner before portioning
For 10 large muffins, use tulip parchment liners in a standard muffin pan and fill the batter to the level of the metal pan rim. For about 15 regular muffins, fill regular liners about three-quarters full.
Use all the pecan crumble
For the large muffins, divide all the crumble evenly among the 10 tops. It will look tall. With regular liners, distribute it evenly up to the top of each liner. Do not press it down.
Check according to size
Begin checking the large tulip-lined muffins at 22 minutes and regular muffins at 18 minutes. Continue until a tester in the muffin center comes out clean or with moist crumbs, without wet batter. These are first-check times, not promises that the muffins are finished.
Cool completely before filling
Let the muffins rest in their pans for 5-10 minutes, then move them to a rack. The centers need to be completely cool before you core them and add chilled mousse.
Step by step
How It All Comes Together
Step 1
Make and chill the pecan crumble
Work the cold butter into the flour, sugars, salt, and vanilla, then stir in the pecans and refrigerate.
Combine the crumble ingredients before working them together. 
The crumble should hold together when squeezed. Step 2
Mix the wet muffin ingredients
Whisk the sugars with the oil, pumpkin, room-temperature yogurt and milk, vanilla, and pumpkin spice emulsion.
Combine the sugars with the wet muffin ingredients. 
Bring the muffin yogurt and milk to room temperature before mixing. 
Use pumpkin puree, as listed in the batter ingredients. Step 3
Add the dry ingredients
Mix just until no dry streaks remain.
Add the dry ingredients to the smooth wet mixture. 
Stop mixing once no dry streaks remain. Step 4
Space the liners and divide the batter
Line alternating cups. Fill tulip liners to the metal pan rim for 10 large muffins, or regular liners about three-quarters full for about 15.
Leave an empty cup between muffins so their tops have room to rise. 
For the large muffins, fill the batter to the level of the metal pan rim. 
The tall tulip liner leaves space above the batter for the generous crumble. Step 5
Add the crumble and bake
Divide all the crumble evenly. Begin checking large muffins at 22 minutes or regular muffins at 18 minutes; bake until the centers are done.
Divide all the crumble evenly among the muffins without pressing it down. 
The muffins should have set centers before they leave the oven. 
Let the muffins cool completely before making the cavities. Step 6
Prepare the cheesecake mousse
Beat the cream cheese and powdered sugar until smooth, then mix in the yogurt, vanilla, salt, mild miso, and sifted unfortified nutritional yeast. Chill until ready to fill.
Sift the unfortified nutritional yeast so it blends evenly. 
The mild miso is an essential part of this cheesecake flavor. 
Beat the cheesecake mixture until smooth. 
Mix the cheesecake mousse until smooth and keep it chilled. 
A tall cup supports the bag while you add the mousse. Step 7
Core the completely cooled muffins
Cut into the center and remove the core without cutting through the bottom.
Cut into the center without going through the bottom. 
Lift out the center while keeping the muffin base intact. Step 8
Pipe in the chilled mousse
Fill each cavity, then keep the muffins refrigerated until serving.
Pipe the chilled mousse into the cooled muffin. 
Keep the piping tip inside the opening as you fill the center. 
Fill each cavity with the chilled cheesecake mousse. Step 9
Pumpkin and cheesecake, ready to enjoy
Peel back the liner and open a muffin to see the creamy center and pecan crumble.
The soft cheesecake filling meets the pumpkin crumb and pecan crumble. Break a muffin open to see the cheesecake center. 
The creamy center is added after the muffin has baked and cooled. 
Keep the filled muffins refrigerated until serving. The cheesecake mousse sits inside the pumpkin muffin beneath the pecan crumble.
Troubleshooting
If This Happens
The topping looks very tall before baking
For the 10 large muffins, divide all the crumble evenly over the tops. Tulip liners support that generous topping. Keep the muffins spaced in alternating cups and do not press the crumble into the batter.
The outside looks done but the center is still wet
The 22-minute and 18-minute checks are starting points for the two sizes. Continue baking until a tester in the center shows clean cake or moist crumbs rather than wet batter.
The mousse softens when it goes into the muffin
The muffins need to be completely cool, and the mousse needs to be chilled. Return the mousse to the refrigerator while the muffins finish cooling.
Before you slice
Texture and serving notes
Serve the muffins with the cheesecake mousse chilled. Peel back the tulip liner and break one open to see the creamy center beneath the pecan crumble.
Keep it good
Storage
Fridge
Store the filled muffins covered in an airtight container in the refrigerator at 40°F (4°C) or below for up to 3 days. Keep the mousse refrigerated while you work and return filled muffins to the refrigerator promptly. Limit time out of refrigeration to 2 hours, or 1 hour when the temperature is above 90°F (32°C).
Freezer
Freeze the completely cooled, baked muffins with their pecan crumble before coring or filling, for up to 2 months. Keep their liners on, wrap each muffin well, and place them in a freezer container or bag without crushing the crumble. Thaw overnight in the refrigerator, still wrapped. Once completely thawed, unwrap, core, and fill with freshly made chilled mousse, then keep refrigerated.
Recipe FAQ
Questions that come up
Do I need a jumbo muffin pan?
I use standard muffin pans with tall tulip parchment liners to make 10 large muffins. Fill the batter to the level of the metal pan rim, then divide all the crumble over the tops. The tulip paper gives the tall tops room.
Can I use regular muffin liners?
Yes. Expect about 15 regular muffins. Fill the liners about three-quarters full with batter, then divide the crumble evenly over them, up to the top of the liners. Begin checking at 18 minutes and keep baking until the muffin centers are done.
Why do you leave empty cups between the muffins?
Lining alternating cups gives the tops room to rise and spread. Use enough pans to keep an empty cup between muffins, or bake in batches.
Can I leave out the miso or nutritional yeast?
Please keep both. The mild miso paste and sifted unfortified nutritional yeast are essential to the cheesecake flavor in this mousse, along with the cream cheese. They are not optional extras in this recipe.
What if I am making these dairy-free?
I highly recommend the two small pinches of food-grade lactic acid powder listed for that version. A little goes a long way. Keep the miso and unfortified nutritional yeast, too. See my dairy-free ingredient picks.
Can I fill the muffins while they are warm?
Let them cool completely first. Warm muffins will soften the chilled mousse. Keep the bottom of each muffin intact when coring so the filling stays inside.
Can I make them ahead?
Yes. Refrigerate the crumble a day ahead, or bake and freeze the unfilled muffins with their crumble. Follow the make-ahead chart for wrapping, thawing, and filling. Filled muffins need to stay refrigerated.
Is there a glaze?
This recipe finishes with pecan crumble and cheesecake mousse. There is no separate glaze.
Should I weigh the ingredients or use volume measurements?
I strongly recommend weighing the ingredients in grams for the most reliable result. Volume measurements are included for convenience, but the amount in a cup can change depending on how an ingredient is filled, packed, or poured. These recipes are easy to follow, but their ratios are precise, so I cannot guarantee the exact same result when volume measurements are used. I still use teaspoons and tablespoons for small amounts like leaveners, salt, spices, and flavorings because those are the most practical measurements.
More recipes to try
- Prep
- About 30 min active (estimated), plus cooling
- Bake
- Until the muffin centers test done; see the size-specific checks
- Total
- Allow time for baking, complete cooling, and filling
- Yield
- 10 large tulip-lined muffins or about 15 regular muffins
Measurement note
For the closest match to the recipe I tested, use grams. Volume measurements are included for convenience, but cups can vary, so I cannot guarantee the exact same result when measuring by volume.
Ingredients
Pecan Crumble
- 125 g all-purpose flour125 g (1 cup + 1 tablespoon) all-purpose flour
- 33 g brown sugar, packed33 g (2 tablespoons + 1 1/2 teaspoons) brown sugar, packed
- 55 g granulated sugar55 g (1/4 cup + 1 teaspoon) granulated sugar
- 1/2 teaspoon fine sea salt1/2 teaspoon fine sea salt
- 100 g cold butter, cubed100 g (7 tablespoons) cold butter, cubed
- Generous 1/2 teaspoon vanilla bean pasteGenerous 1/2 teaspoon vanilla bean paste
- 55 g chopped pecans55 g (1/2 cup) chopped pecans
Muffins - Dry Ingredients
- 300 g all-purpose flour300 g (about 2 1/2 cups) all-purpose flour
- 2 teaspoons baking powder2 teaspoons baking powder
- 1/4 teaspoon baking soda1/4 teaspoon baking soda
- 3/4 teaspoon + a small pinch fine sea salt3/4 teaspoon + a small pinch fine sea salt
- 1/2 teaspoon ground cinnamon1/2 teaspoon ground cinnamon
- 1/8 teaspoon ground cardamom1/8 teaspoon ground cardamom
- 1/4 teaspoon ground nutmeg1/4 teaspoon ground nutmeg
- Pinch ground gingerPinch ground ginger
Muffins - Wet Ingredients
- 140 g dark brown sugar, packed140 g (about 2/3 cup) dark brown sugar, packed
- 100 g granulated sugar100 g (1/2 cup) granulated sugar
- 132 g neutral oil132 g (1/2 cup + 1 tablespoon + 2 teaspoons) neutral oil
- 210 g pumpkin puree210 g (3/4 cup + 2 tablespoons) pumpkin puree
- 130 g plain unsweetened Greek-style yogurt, room temperature130 g (1/2 cup + 2 1/2 teaspoons) plain unsweetened Greek-style yogurt, room temperature
- 115 g milk, room temperature115 g (scant 1/2 cup) milk, room temperature
- 1 tablespoon + 1/4 teaspoon vanilla bean paste1 tablespoon + 1/4 teaspoon vanilla bean paste
- 1/2 teaspoon pumpkin spice emulsion1/2 teaspoon pumpkin spice emulsion
Cheesecake Mousse
- 284 g cream cheese284 g (1 1/4 cups) cream cheese
- 90 g powdered sugar90 g (3/4 cup) powdered sugar
- 1/2 teaspoon unfortified nutritional yeast, sifted1/2 teaspoon unfortified nutritional yeast, sifted
- 1/4 teaspoon mild white or yellow miso paste1/4 teaspoon mild white or yellow miso paste
- 2 small pinches food-grade lactic acid powder, if making dairy-free2 small pinches food-grade lactic acid powder, if making dairy-free
- 3/4 teaspoon vanilla extract3/4 teaspoon vanilla extract
- 53 g plain unsweetened yogurt53 g (3 tablespoons + 2 1/2 teaspoons) plain unsweetened yogurt
- 2 small pinches fine sea salt2 small pinches fine sea salt
Pan used
Standard muffin pans with alternating cups lined. Use tall tulip parchment liners for 10 large muffins, or regular liners for about 15 muffins.
Instructions
- 1Preheat the oven to 350°F (175°C). Line alternating cups of standard muffin pans, leaving an empty cup between muffins so their tops have room to rise. Use tall tulip parchment liners for 10 large muffins or regular paper liners for about 15 regular muffins.
- 2Make the pecan crumble: combine the all-purpose flour, brown sugar, granulated sugar, and salt. Add the cold cubed butter and vanilla bean paste. Work together with your fingertips until evenly combined and the mixture holds together when squeezed. Stir in the chopped pecans and refrigerate while making the batter.
- 3In a large bowl, whisk the dark brown sugar, granulated sugar, oil, pumpkin puree, room-temperature Greek-style yogurt and milk, vanilla bean paste, and pumpkin spice emulsion until smooth.
- 4Whisk together the all-purpose flour, baking powder, baking soda, salt, cinnamon, cardamom, nutmeg, and ginger. Add to the wet ingredients and gently mix just until no dry streaks remain.
- 5For the 10 large tulip-lined muffins, divide the batter among the liners, filling to the level of the metal pan rim. For about 15 regular muffins, fill regular liners about three-quarters full.
- 6Divide all the chilled pecan crumble evenly over the muffins without pressing it down. The crumble will look tall on the large muffins. For regular liners, distribute it up to the top of the liners.
- 7Bake at 350°F (175°C). Begin checking the large tulip-lined muffins at 22 minutes or regular muffins at 18 minutes. Continue baking until a tester inserted into the muffin center comes out clean or with moist crumbs, without wet batter. These are first-check times, not fixed finished bake times.
- 8Let the muffins cool in the pans for 5-10 minutes, then carefully transfer them to a wire rack and cool completely before coring or filling.
- 9Make the cheesecake base: beat the cream cheese until smooth. Add the powdered sugar and mix until smooth. Mix in the sifted unfortified nutritional yeast, mild miso paste, vanilla extract, plain unsweetened yogurt, and salt. If making the dairy-free version, add the two small pinches of food-grade lactic acid powder.
- 10Cover and refrigerate the finished mousse until the muffins are completely cool and ready to fill.
- 11Use a small round cutter or a wide piping tip to cut into the center of each cooled muffin without cutting through the bottom. Lift out the core with a small spoon, keeping the base and sides intact.
- 12Transfer the chilled mousse to a piping bag and pipe it into each cavity. Keep the mousse chilled while you work, then cover and refrigerate the filled muffins until serving.
Helpful notes
- I use tall tulip parchment liners in standard muffin pans for 10 large muffins. Fill the batter to the level of the pan rim and divide all the crumble evenly among them. It will look tall, which is the look shown in the photos.
- With regular liners, fill about three-quarters full with batter and add crumble up to the top of the liners. Expect about 15 regular muffins.
- Line alternating cups so there is an empty cup between muffins. Begin checking large muffins at 22 minutes or regular muffins at 18 minutes, then use the center tester check to decide when they are finished.
- Please do not leave these out. They are essential to the cheesecake flavor I worked so long to get. Use mild white or yellow miso and sift the unfortified nutritional yeast.
- For the dairy-free version, I highly recommend two small pinches of food-grade lactic acid powder in the mousse. A little goes a long way.
- Cool the muffins completely before coring and filling. Keep the bottom intact so the mousse stays inside.
- Store the filled muffins covered in an airtight container in the refrigerator at 40°F (4°C) or below for up to 3 days. Keep the mousse refrigerated while you work and return filled muffins to the refrigerator promptly. Limit time out of refrigeration to 2 hours, or 1 hour when the temperature is above 90°F (32°C).
- Freeze the completely cooled, baked muffins with their pecan crumble before coring or filling, for up to 2 months. Keep their liners on, wrap each muffin well, and place them in a freezer container or bag without crushing the crumble. Thaw overnight in the refrigerator, still wrapped. Once completely thawed, unwrap, core, and fill with freshly made chilled mousse, then keep refrigerated.
Meet the baker
Angela Heckler
Angela Heckler is the recipe developer, baker, and photographer behind Obsessed Cakes. Her Old-Fashioned Donut Loaf series is a growing collection of cake-donut-inspired loaves with soft, deeply moist crumbs, buttery streusel, and crackly glaze. Angela develops and tests every recipe in her Arizona kitchen. Follow Obsessed Cakes on Instagram, TikTok, and YouTube.
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