These Pumpkin Cheesecake Cups are a creamy, lightly spiced fall dessert made with homemade pumpkin puree and dripped SCD yogurt instead of cream cheese. Naturally sweetened with honey, they’re baked in a water bath for a smooth custard-like texture. This recipe is flexible: you can use pie pumpkins, heirloom varieties like White Pie Pumpkin or Hot Chocolate Pumpkin, or even butternut squash. Each adds its own flavor while keeping the cheesecake cups wholesome and satisfying. Whether you’re following the Specific Carbohydrate Diet (SCD) or just want a healthier twist on cheesecake, these little cups make the perfect seasonal treat.
A Different Take on Pumpkin Cheesecake
White Pie Pumpkin Flavor Notes
The White Pie Pumpkin is like a gentler cousin of the orange pie pumpkin. It’s milder, lightly sweet, and surprisingly delicious roasted on its own with just butter, salt, and pepper. Once pureed, it makes a soft, lightly sweet base that blends beautifully into cheesecake.
Hot Chocolate Pumpkin Flavor Notes
The Hot Chocolate Pumpkin stands out with its light brown skin and deeper, layered flavor. I cooked mine whole in the Instant Pot (step-by-step guide here and video tutorial), which produced a smoother puree than roasting. Its earthy notes reminded me faintly of tea or even chocolate. Subtle, smooth, and complex without being overpowering.
Other Pumpkin & Squash Options
Don’t limit yourself to specialty pumpkins. This recipe works beautifully with canned pumpkin, butternut, acorn, or Hubbard squash. Each variation gives the cheesecake cups a slightly different twist.
How to Make Pumpkin Cheesecake Cups
The full recipe card is below, but here’s the quick overview:
1. Drip the yogurt
Start with 2–3 cups of homemade yogurt made from half & half or whole milk. Place it in a yogurt strainer and let it drip in the refrigerator for 24 hours. This will reduce it to about 1 to 1 1/2 cups of very thick yogurt with a cream cheese–like texture.
- I use a yogurt strainer because it’s easy and mess-free.
- If you don’t have one, line a strainer with cheesecloth, a nut milk bag, or a thin dish towel set over a bowl to catch the whey.
2. Blend the filling
Combine the dripped yogurt with pumpkin puree, eggs, honey, vanilla, lemon juice, and warm spices. Blend until smooth and creamy.
3. Bake in a water bath
Divide the mixture into six 8-ounce ramekins. Place them in a 9×13 casserole dish and pour hot water into the dish until it reaches halfway up the ramekins. Bake at 350°F for 60–70 minutes, checking at 50 minutes. The edges should be set while the centers remain slightly soft.
4. Cool and chill
Remove ramekins from the water bath, let cool completely, and refrigerate until fully chilled for the best creamy texture.
This method gives you perfectly portioned cheesecakes with a silky, custard-like consistency and no need for a crust.
Tips & Variations
- Bake as a Whole Cheesecake: Pour the batter into a 9-inch round or springform pan. Wrap the outside in foil, place on a baking sheet, and bake for the same amount of time. You can add a crust if you like, but because the yogurt base releases some liquid, the crust may become soggy. This is one reason I prefer making the cups.
- Spice Adjustments: Adjust the spice blend to suit your taste. Add more cinnamon for warmth, more ginger for bite, or skip cloves if you prefer a softer flavor.
- Topping Ideas: Serve plain, or add a drizzle of honey, a sprinkle of cinnamon, or a dollop of dripped yogurt. Fresh berries also pair nicely.
- Make Ahead: These cheesecake cups taste even better the next day as the flavors meld and the texture sets more firmly.
FAQ: Pumpkin Cheesecake Cups
Can you make cheesecake with yogurt instead of cream cheese?
Yes. Dripped yogurt (sometimes called yogurt cheese) works beautifully in place of cream cheese. When made with half & half or whole milk, and dripped for 24 hours, the texture becomes thick, creamy, and slightly tangy, very similar to cream cheese but lighter and easier to digest.
What kind of pumpkin works best for pumpkin cheesecake?
Any pumpkin puree will work in this recipe. Pie pumpkins are the classic choice, but heirloom varieties like White Pie Pumpkin or Hot Chocolate Pumpkin add unique flavors. You can also use butternut, acorn, or hubbard squash, or even canned pumpkin for convenience.
How do I know when cheesecake cups are done baking?
Check around the 50-minute mark. The edges should be set, while the centers may still have a slight wobble. This is normal, and the cheesecake will firm up as it cools. Overbaking can lead to cracks or a dry texture, so it’s best to remove them when they’re just set.
Can I bake this recipe as a whole cheesecake?
Yes. Pour the mixture into a 9-inch round or springform pan, wrap the outside in foil, and place on a baking sheet. Bake for 60–70 minutes, just like the cups. You can use a crust if you like, but since the yogurt base releases liquid, the crust may become soggy. The ramekin method avoids this issue and creates perfectly portioned servings.
Pumpkin Cheesecake Cups (SCD Yogurt Based Recipe)
Equipment
Ingredients
- 2 cups pumpkin puree
- 1½ cups SCD yogurt (dripped to be thick like cream cheese)
- ½ cup honey
- 1 tsp lemon juice
- 1 tsp vanilla
- 1 tsp cinnamon
- ½ tsp nutmeg
- ¼ tsp cloves
- ¼ tsp ginger
- ¼ tsp allspice
- ¼ tsp salt
Instructions
- Preheat oven to 350℉ / 180℃
- In a mixing bowl, combine pumpkin puree, dripped yogurt, eggs, honey, vanilla, lemon juice, and spices.
- Whisk until smooth
- Place six 8-ounce ramekins in a 9×13 casserole dish.
- Divide the pumpkin mixture evenly among the ramekins.
- Pour room temperature water into the casserole dish until it reaches halfway up the sides of the ramekins.
- Bake for 60–70 minutes, checking at 50 minutes. The edges should be set while the centers remain slightly soft.
- Remove ramekins from the water bath, cool completely, then refrigerate until chilled before serving.
Notes
- Dripped Yogurt: Prepare ahead of time. Start with about 3 cups of yogurt made from half & half or whole milk. Strain for 24 hours in a yogurt strainer, cheesecloth, nut milk bag, or thin dish towel set over a bowl. This will yield 1–1 1/2 cups of very thick yogurt.
- Pumpkin Puree: Prepare ahead by roasting or cooking in the Instant Pot and pureeing, or use canned (SCD friendly) pumpkin.
- Whole Cheesecake Option: Pour into a 9-inch springform pan, wrap the outside in foil, and bake in the same water bath for 60–70 minutes. A crust can be used, but the yogurt base releases some liquid which may cause sogginess.
- Make Ahead: These cheesecake cups taste even better the next day after chilling.
Nutrition
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