Homemade Mini Pumpkin Cheesecakes in a Muffin Tin

Let me introduce you to these Mini Pumpkin Cheesecakes, a satisfying dessert that’s perfectly bite-sized, creamy, and packed with fall flavor. Each one has a sweet graham cracker crust and a spiced pumpkin filling that’s rich and creamy with just the right amount of sweetness. They’re exactly what you need when you want a cozy seasonal dessert without the fuss of a whole cheesecake.

These little cheesecakes are not just delicious, they’re also incredibly versatile. They can be used to impress the in-laws and whole family, or made just for yourself to enjoy the pumpkin season. You can even top them with different garnishes for added texture and visual flair.

Whether you’re making them as a Thanksgiving dessert, for a weekend brunch, or as a sweet treat for you, these mini pumpkin desserts won’t disappoint. And the best part is, they’re easier to make than you might think. You don’t need a springform pan wrapped in aluminum foil, and it takes way less time than a regular-sized cheesecake.

Since you are here and love a delicious pumpkin recipe, check out these Pumpkin Cheesecake Bars. You might also like these Mini Cheesecakes with Oreo Crust, these No Bake Cheesecake Bars with Vanilla Beans, this Pecan Pie Cheesecake Bars Recipe, or these Crumbl Chocolate Pumpkin Cheesecake Cookies.

Ingredients for this mini pumpkin cheesecake recipe

Here are the ingredients you will need to make these bite-sized versions of a creamy pumpkin cheesecake. Scroll down to the recipe card at the bottom of the page for the detailed ingredient measurements.

Crust

• Graham Cracker Crumbs: form the crust that holds your cheesecakes together.
• Granulated Sugar: sweetens the crust.
• Unsalted Butter: binds the crust crumbs together. You’ll want it melted.
• **Optional: Speculoos or gingersnap cookies are a delicious swap for graham crackers if you want a bolder crust with extra fall flavor.

Filling

• Full fat Cream Cheese: is the base of the cheesecakes.
• Pumpkin Purée: adds that deep pumpkin flavor.
• Sour Cream: balances the sweetness and gives a little tang.
• Light Brown Sugar and Granulated Sugar: add sweetness to the mixture. You can use dark brown sugar instead of light if you really like the molasses flavor.
• Whole Egg and Egg Yolk: provides structure and helps the cheesecakes hold their shape.
• Vanilla Extract: enhances all the warm spices.
• Molasses: deepens the flavor with a touch of smoky sweetness.
• Cinnamon: is the main spice star.
• Ground Ginger, Nutmeg, Cloves: create our homemade pumpkin spice mix.
• All-purpose Flour: helps stabilize the batter and prevent cracking.
• Heavy Cream: adds extra silkiness for a more luscious and creamy cheesecake base.

How to make mini pumpkin cheesecakes in a muffin tin

This is how you can make this adorable mini pumpkin cheesecakes recipe. Make sure to scroll down to the recipe card at the end of this post for the oven temp, baking time, and full step-by-step instructions! 

1. Preheat your oven and line a 12-cup muffin tin with paper liners. Lightly spray each muffin liner with nonstick spray.
2. In a medium bowl, mix together the graham cracker crumbs, sugar, and melted butter. Or use any spiced cookie crumbs you like instead of the graham crackers.

3. Press about 1 heaping tablespoon of the crumb mixture firmly into the bottom of each liner. Bake for a few minutes, then remove from the oven and let cool while you make the filling.

4. Beat the cream cheese with a stand mixer or hand-held mixer until smooth and creamy. Add the pumpkin puree, sour cream, molasses, brown sugar, granulated sugar, and vanilla extract. Beat again with a hand mixer until fully combined, scraping down the sides as needed.
5. Switch the electric mixer to low speed and add the egg and egg yolk one at a time. Mix just until incorporated and avoid overmixing.

6. Gently fold in the spices, flour, and heavy cream with a rubber spatula until the cream cheese mixture is smooth and uniform.
7. Spoon the filling evenly over the pre-baked crusts. Tap the pan gently on the counter to level the batter.

8. Fill a large baking sheet with just enough hot water to cover the surface and place the filled muffin tin inside. This is our water bath, which will help the mini cheesecakes not crack.
9. Bake until the edges are set but the centers still jiggle slightly. Then turn the oven off and leave the door slightly ajar for 20 minutes to help prevent cracks.
10. Remove the pan from the oven and let the mini cheesecakes cool on a wire rack. Refrigerate for at least 3 hours or overnight for the best creamy texture.

Why do you need to make these Mini Pumpkin cheesecakes?

• This fall recipe is the best way to get the perfect size for serving large groups at dinner parties during the holidays.
• These mini desserts are full of pure autumn and fall flavors in every bite.
• They’re impressive and visually appealing yet easy to make.
• It’s the perfect fall dessert for a holiday gathering, brunch, or just a weeknight treat.
• The decadent pumpkin cheesecake filling and classic graham cracker crust rival any bakery cheesecake, without leaving your kitchen.

Frequently asked questions – FAQ

How do I turn whole graham crackers into crumbs?

The easiest way is to blend them in a food processor until you have fine crumbs. If you don’t have one, you can seal them in a plastic bag, place them on the countertop, and lightly tap them with a rolling pin.

What can I top these mini pumpkin cheesecake bites with?

• A dollop of whipped cream for a light and airy sweetness. Canned is convenient, but homemade whipped cream has a better look and flavor.
• A sprinkle of ground cinnamon for aroma and color. Flaky sea salt works too.
• A drizzle of butterscotch, dulce de leche, or salted caramel sauce adds a sweet-salty contrast that pairs perfectly with pumpkin and cream cheese.
• Crumbled gingersnaps, speculoos cookies, or pecans give texture and crunch.
• A few teaspoons of caramel sauce right on top of the cooled down cheesecakes like I did below and a dollop of whipped cream.

Can I use pumpkin pie filling instead of puree?

Unfortunately no. A classic pumpkin pie mix wouldn’t have the texture we’re looking for in a cheesecake.

Can I make these ahead of time?

Absolutely! You can prepare them a day or even two in advance. It’s actually a smart idea because the flavors will deepen and taste better as it sits overnight.

How do I store the leftovers?

Once fully cooled, wrap each cheesecake individually in plastic wrap and place in an airtight container. You can refrigerate for 3-4 days or freeze for up to 2 months. If you keep them in the freezer, thaw in the refrigerator overnight before serving.

How do I prevent cracks in the filling?

The three steps to avoid cracks:

1. Make sure your cream cheese and eggs are at room temperature.
2. Mix eggs in gently and avoid overmixing or incorporating too much air.
3. A hot water bath is a MUST! Don’t skip it or they will crack.
4. Letting the cheesecakes cool gradually helps prevent cracking. First, keep them in the oven with the heat turned off and the door ajar, then let it reach room temperature, and finally move it to the fridge.

If you follow these rules, your tiny treats should come out perfectly!

How can I adjust the flavor?

Try reducing the brown sugar by 1–2 tablespoons if you prefer a less-sweet cheesecake. Add 1–2 teaspoons of pumpkin pie spice for a more pronounced pumpkin taste. Don’t make too many tweaks, as this recipe might not turn out how it did for me.