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These mini pumpkin cheesecakes are the perfect make-ahead Thanksgiving dessert. With a creamy pumpkin filling and a chocolate crust, these mini cheesecakes can even be made gluten free. 

Two stacked mini pumpkin cheesecakes. The top one is unwrapped and has a bite taken out of it.

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Now that October is nearly over, it’s time to start thinking about Thanksgiving.

Ok, maybe I was already thinking about Thanksgiving. What can I say, I love planning my Thanksgiving menu! 

From sides like garlic mashed potatoes and cranberry fluff to desserts like mini pecan pies and these mini pumpkin cheesecakes, it’s the best meal of the year.

This recipe comes from my friend Erin over at Texanerin Baking and is a great mini cheesecake twist on pumpkin cheesecake. With a gluten-free chocolate crust, this is a recipe everyone will adore!

Mini pumpkin cheesecakes topped with chocolate ganache on a wire cooling rack.


Have you ever tried pumpkin and chocolate together? It might sound like an unexpected combination, but it’s so good!

Just give my pumpkin brownies and try and see what I mean.

These mini pumpkin cheesecakes have a perfectly spiced pumpkin filling on top of a chocolate cookie crust. I also like to top them with a bit of chocolate ganache just before serving. I think it’s pretty and it adds some extra chocolate to the mix!

The crust is adapted from mini peanut butter cheesecakes and has three options:

All three versions are equally delicious, so use whatever works best for you!

Mini pumpkin cheesecake ingredients arranged on a brown countertop.

More crust options

If you don’t need the crust to be gluten-free and you want to stick with the pumpkin and chocolate combination, you can use an Oreo cookie crust, like what I make for my chocolate cheesecake.

If you don’t like the pumpkin and chocolate combo, you could use a classic graham cracker crust (like what I use for my classic mini cheesecakes), a gingersnap crust like I use for no-bake cranberry cheesecake, or use the almond-flour-based crust from gluten-free mini cheesecakes for a gluten-free version.

If you use the last option, leave out the lemon zest and add about a teaspoon of cinnamon and maybe a pinch of ground ginger.

You can also swap out the chocolate ganache topping with salted caramel sauce if you’d like! 

Mini chocolate crusts in a lined cupcake pan.


If making cheesecake intimidates you, don’t let it! I promise that it is much easier than you think. And sometimes making mini cheesecakes is a great way to start.

Gluten-free option

As I mentioned above, this recipe has an option for a standard crust with all-purpose flour or two gluten-free options.

Pumpkin cheesecake filling in a white mixing bowl.

If you need to make the gluten-free version, you can substitute the 6 tablespoons of all-purpose flour in the crust with either:

  • 6 tablespoons gluten-free measure-for-measure (or 1-for-1) baking flour, OR
  • 6 tablespoons buckwheat flour

When baking, the crust may look very bubbly and even soupy, especially if you use the buckwheat flour. 

It’s the weirdest thing – but it works out in the end! 

Keep in mind that this crust recipe will not work in a regular pie pan or springform pan; it will only work for mini cheesecakes.

Unbaked mini pumpkin cheesecakes in a cupcake pan, ready to go in the oven.

Making this recipe

Start making these mini pumpkin cheesecakes by working on the crust. 

Whisk together the sugar, flour (either all-purpose or gluten-free), cocoa powder, and salt. Use an electric mixer to beat in the butter until a sticky dough forms.

Line  a standard muffin tin with cupcake liners and divide the dough evenly between the cups. It’ll be about 1 tablespoon per cup.

Baked mini pumpkin cheesecakes in a cupcake pan, fresh from the oven.

Use the bottom of a small glass (I use a shot glass) to press the dough down, then bake.

After baking and cooling for a minute, you’ll want to use the same glass to lightly press the crusts down again to remove any holes. Let cool for 10 minutes while you make the filling.

To make the pumpkin filling, beat the cream cheese with an electric mixer until light and fluffy, then add the sugars, molasses, pumpkin, vanilla, salt, and pumpkin pie spice. Mix on low until well combined.

Three mini pumpkin cheesecakes on a speckled plate. The front cheesecake is unwrapped. All of them are topped with chocolate ganache.

Add the eggs one at a time, mixing after each addition until well combined.

Add the filling on top of the cooled crusts. Using a large cookie scoop makes this easy! 

After baking, let the cheesecakes cool in the pan, then refrigerate for at least 2 hours before serving. 

Mix together the ganache, then let it cool for 20-30 minutes before serving with the cooled cheesecakes.

Three mini pumpkin cheesecakes on a plate. One of them is unwrapped and has a bite taken out of it.


I made these gluten-free mini pumpkin cheesecakes back in September and have been enjoying one a week from the freezer. 

For those of you who want to get as much of their Thanksgiving preparation done in advance as possible, these are perfect!

I used to try to time everything so that all the food, including dessert, would be piping hot and fresh from the oven. Luckily, I’ve seen the errors in my ways and now prepare as much as possible in advance!

Three mini pumpkin cheesecakes, each topped with chocolate ganache, arranged on a plate.

If you want to make these cheesecakes the week of Thanksgiving, simply store them in the refrigerator in an airtight container for up to 3 days.

If you want to make them more than 3 days in advance, place the cooled cheesecakes in an airtight container and freeze for up to a month. 

To thaw, place the mini pumpkin cheesecakes in the refrigerator overnight. They’ll be ready to top with the ganache just before serving for Thanksgiving dessert! 

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Mini Pumpkin Cheesecakes

By: Erin
5 from 2 ratings
Prep: 45 minutes
Cook: 23 minutes
Cooling Time: 3 hours
Total: 4 hours 8 minutes
Servings: 12 mini cheesecakes
These mini pumpkin cheesecakes are the perfect make-ahead Thanksgiving dessert. With a creamy pumpkin filling and a chocolate crust, these mini cheesecakes can even be made gluten free. 


For the Crust

  • 6 tablespoons granulated sugar
  • 6 tablespoons all-purpose flour or gluten-free 1-to-1 baking flour OR buckwheat flour for a gluten-free version
  • 6 tablespoons cocoa powder
  • pinch of salt
  • 4 ½ tablespoons unsalted butter softened

For the Cheesecake

  • 8 ounces cream cheese room temperature
  • ¼ cup brown sugar
  • ¼ cup granulated sugar
  • 1 tablespoon molasses
  • 1 cup canned pure pumpkin puree not pumpkin pie filling
  • 1 teaspoon pure vanilla extract
  • pinch of salt
  • 2 ½ teaspoons pumpkin pie spice
  • 3 large eggs

For the Ganache

  • ¼ cup whipping cream or heavy cream
  • ½ cup semi-sweet chocolate chips


  • Preheat the oven to 350°F and line a muffin pan with 12 muffin liners. Note that this crust recipe does not work in regular pie pans and only as mini cheesecakes.
  • In a large mixing bowl, mix together the sugar, flour, cocoa powder, and salt. Using an electric hand mixer, beat in the butter at low speed until thoroughly combined and a dough forms. If you have trouble incorporating it, use your hands. It’ll be sticky.
  • Divide the dough between the muffin liners (I used 19 grams of dough per liner, or about 1 tablespoon). Press the dough down with the bottom of a shot glass. If using gluten-free 1-to-1 baking flour or all-purpose flour, bake for 11-13 minutes. Move on to the next step. If using buckwheat, bake for 14 minutes. The crusts will appear very bubbly and liquid. Remove from the oven, let cool for a minute, and then use the shot glass again to lightly press down (which will remove the holes).
  • After baking, the crust will still be soft but will firm slightly as it cools. Let cool for 10 minutes while you prepare the cheesecake.

For the Cheesecake

  • Turn the oven down to 325°F.
  • With an electric hand mixer, beat the cream cheese at medium speed until light and fluffy.
  • Add the brown sugar, granulated sugar, molasses, pumpkin puree, vanilla extract, salt and pumpkin pie spice and beat on low until well combined.
  • Add the eggs one at a time, beating on low after every addition until thoroughly incorporated. Do not over mix!
  • Fill each muffin liner to the top with cheesecake batter and bake for 20-23 minutes or until the middles of the cheesecakes are set and don’t jiggle when the pan is tapped.
  • Remove from the oven and let the cheesecakes cool in the pan.
  • Once completely cool (about 1 hour), remove the cheesecakes from the pan and refrigerate for at least 2 hours or until ready to serve. The wrappers come off neatly before and after refrigeration.
  • Refrigerate the cheesecakes in an airtight container for up to 3 days.

For the Ganache

  • In a small saucepan over medium-low heat, warm the cream just until hot, steamy and on the verge of simmering. Remove from the heat.
  • Pour this over the chocolate chips and stir until all the chocolate chips are completely melted.
  • Let cool for about 20-30 minutes or until room temperature before pouring over the chilled cheesecakes.



Helpful resources:


Serving: 1mini cheesecake, Calories: 270kcal, Carbohydrates: 27g, Protein: 4g, Fat: 17g, Saturated Fat: 10g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 5g, Trans Fat: 0.2g, Cholesterol: 77mg, Sodium: 82mg, Potassium: 207mg, Fiber: 2g, Sugar: 20g, Vitamin A: 3700IU, Vitamin C: 1mg, Calcium: 53mg, Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

5 from 2 votes (2 ratings without comment)

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  1. Amanda says:

    Making these for my daughters first birthday. Going to use maple syrup and maple sugar instead. Question, she’s allergic to egg whites. Is there an alternative(chick pea water or ground flaxmeal?) or can I get away with only egg yokes for this recipe? Thank you!

    I <3 #mybakingaddiction :)

    1. Jamie says:

      Hi Amanda-
      I have honestly never tried these with an egg substitute so I am not sure how that would work.

  2. Becky says:

    I was trying to decide how to make mini pumpkin cheesecakes a little different from the ones I made last year, when this recipe came in my e-mail. They were perfect and my mom who doesn’t like cheesecake agreed!
    Thank you for the inspiration and lovely recipes!

  3. Patty says:

    Wondering if you used light or dark brown sugar?

    1. Jamie says:

      I usually have light brown sugar on hand, but you really could use either. Dark brown will just give you a richer molasses flavor, so it’s up to you! Happy baking –

  4. Sue says:

    How does this recipe translate to the cheesecakes in a 3″ diameter size with six per pan?
    Sounds delicious. I have celiac so it would work along with your Mini-Cheesecake recipe.

    1. Jamie says:

      Hi, Sue! Are you wanting to half the recipe? Let me know how I can help!

  5. Dieselle says:

    Decieded to make mini cheesecakes, sans chocolate bottom, will top with the ganache. Let you know how they turn out.

    1. Jamie says:

      Please do, Dieselle!