The aroma of fall wafts through my kitchen as I prepare these Skinny Mini Pumpkin Cheesecakes, a delightful escape from traditional holiday desserts. With a luscious creamy pumpkin filling nestled in a crunchy pecan crust, these mini treats not only look adorable but shine as a gluten-free and refined sugar-free option. They come together effortlessly, making them perfect for those busy weeks filled with festivities. As the flavors meld and the warm spices fill the room, you’ll find that these healthier desserts are the ultimate guilt-free indulgence. Who could resist a sweet treat that captures the essence of the season while being so easy to whip up? Curious to discover how simple it is to create these delightful bites? Let’s dive into the recipe!

Why Are These Mini Cheesecakes Special?
Simplicity at its finest: With just a handful of ingredients, you can whip up these delightful Skinny Mini Pumpkin Cheesecakes without any hassle.
Guilt-free indulgence: These treats are not only flavorful but also gluten-free and refined sugar-free, making them a healthier dessert option that your guests will adore.
Perfectly sized: Their mini portions make them ideal for holiday gatherings, allowing everyone to savor a sweet bite without overindulging.
Rich, creamy flavor: The combination of pumpkin puree and Greek yogurt results in a smooth, luxurious texture that melts in your mouth.
Versatility delights: Feel free to explore variations like adding mini chocolate chips or swapping pecans for walnuts to customize each bite!
Whether serving them alongside a warm cup of coffee or as a delightful ending to festive meals, these cheesecakes will surely become a go-to dessert, just like Pumpkin Cheesecake Truffles or Pumpkin Cream Cheese treats!
Skinny Mini Pumpkin Cheesecakes Ingredients
For the Pecan Crust
- Pecan Nuts – Provides a crunchy base that enhances the cheesecake’s flavor; can substitute with finely chopped walnuts if desired.
- Maple Syrup or Honey – Acts as a natural sweetener for both the crust and filling; feel free to replace with brown sugar for a different taste.
- Water – Helps bind the crust ingredients together for a firm texture.
- Unsalted Butter (melted) – Adds rich flavor to the crust; using unsalted gives you better control over the saltiness.
For the Cheesecake Filling
- Reduced Fat Cream Cheese – Forms the creamy base of the cheesecake; regular cream cheese can be used for a richer flavor.
- Greek Yogurt (2%) – Adds creaminess and lightness to the filling; switch to vanilla Greek yogurt for a subtle twist.
- Pumpkin Puree – Essential for that authentic pumpkin flavor in your Skinny Mini Pumpkin Cheesecakes.
- Pumpkin Spice Seasoning – Adds the signature warm spice profile; a homemade mix of cinnamon, ginger, nutmeg, allspice, and cloves works beautifully as a substitute.
- Vanilla Extract – Elevates the overall sweetness and adds depth to the flavor.
- Egg – Binds the cheesecake filling together, providing structure for those perfectly mini treats.
Step‑by‑Step Instructions for Skinny Mini Pumpkin Cheesecakes
Step 1: Preheat the Oven
Begin by preheating your oven to 325°F (165°C). While it’s heating, prepare a muffin tin by lining it with cupcake liners, giving each liner a light spray of non-stick spray. This will ensure that your delicious Skinny Mini Pumpkin Cheesecakes come out easily after baking.
Step 2: Prepare the Pecan Crust
In a mixing bowl, combine chopped pecans, maple syrup (or honey), water, and melted unsalted butter. Stir until the mixture is well blended. Firmly press this mixture into the bottom of each cupcake liner, creating a solid base for your mini cheesecakes. Aim for an even layer that is slightly compacted.
Step 3: Bake the Crust
Place the muffin tin in the oven and bake the crust for about 13-14 minutes. You’ll know it’s done when the edges are slightly browned, and the crust feels firm to the touch. Once baked, remove it from the oven and allow it to cool slightly while you prepare the filling.
Step 4: Make the Cheesecake Filling
In a large mixing bowl, beat the reduced fat cream cheese until it’s smoothly blended. Add the Greek yogurt, maple syrup (or honey), pumpkin puree, pumpkin spice seasoning, and vanilla extract. Mix until everything is well combined and creamy, then gently fold in one egg, being careful not to overbeat. This will help maintain the cheesecake’s texture.
Step 5: Fill Each Crust
Now it’s time to fill each prepared pecan crust! Spoon the cheesecake batter into the cupcake liners, filling them nearly to the top. This will give your Skinny Mini Pumpkin Cheesecakes a lovely, rounded shape as they bake.
Step 6: Bake the Cheesecakes
Increase the oven temperature to 350°F (175°C). Place the muffin tin back in the oven and bake for 17-20 minutes. The center of each cheesecake should be slightly jiggly when done; this indicates that they are perfectly baked and will set as they cool.
Step 7: Cool and Refrigerate
Once baked, remove the muffin tin from the oven and let the cheesecakes cool at room temperature for 30 minutes. Then, carefully transfer the mini cheesecakes to an airtight container and refrigerate for at least two hours, or until fully chilled. This cooling time allows the flavors to develop beautifully.

How to Store and Freeze Skinny Mini Pumpkin Cheesecakes
Fridge: Store your Skinny Mini Pumpkin Cheesecakes in an airtight container for up to 5-6 days. This keeps them fresh and ready to enjoy as a delightful treat.
Freezer: For longer storage, freeze the cheesecakes in an airtight container or wrapped separately in plastic wrap for up to 2 months. Thaw overnight in the fridge before serving.
Reheating: If you prefer a slightly warmer dessert, let the mini cheesecakes sit out at room temperature for about 15 minutes before serving. They’re best enjoyed chilled but can be adapted to your taste!
Skinny Mini Pumpkin Cheesecake Variations
Feel free to get creative with these variations, adding your personal touch to this delightful recipe!
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Walnut Crust: Swap out pecans for walnuts to achieve a different nutty profile and subtle flavor twist.
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Dairy Option: Use regular yogurt instead of Greek yogurt for a creamier filling that retains all the pumpkin goodness without the extra tang.
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Chocolate Delight: Add mini chocolate chips to the cheesecake batter, creating a scrumptious surprise that chocolate lovers will crave.
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Spiced Up: Boost the flavor by adding a pinch of cayenne pepper to the filling for a surprising kick that pairs well with pumpkin spice.
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Vegan Swap: For a vegan version, substitute the cream cheese with a plant-based cream cheese and use a flax egg or chia seed egg instead.
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Flavor Infusion: Try incorporating orange zest into the cheesecake filling for a refreshing citrus note that perfectly complements the warmth of pumpkin spice.
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Sugar-Free: If you’re looking for an even lower sugar option, use a sugar substitute like erythritol in place of maple syrup or honey.
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Toppings Layer: Top your mini cheesecakes with a dollop of homemade whipped coconut cream and a sprinkle of cinnamon for an extra touch of indulgence.
With so many variations at your fingertips, you can enjoy these Skinny Mini Pumpkin Cheesecakes in an array of delicious styles! And if you want to explore more pumpkin-inspired treats, check out Pumpkin Cream Cheese muffins or Healthy Pumpkin Oat cookies that are perfect for the season.
Expert Tips for Skinny Mini Pumpkin Cheesecakes
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Egg Handling: Avoid overbeating the egg in the filling; this helps maintain a smooth texture and prevents the cheesecakes from becoming overly airy.
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Crust Cooling: Allow the crust to cool slightly before removing from the muffin tin. This simple step reduces stickiness and ensures a clean lift.
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Serving Temperature: These mini cheesecakes are best served chilled. The flavors meld beautifully and the texture becomes even more delightful when they’re cold.
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Ingredient Substitutions: Don’t hesitate to swap pecans for walnuts or use regular yogurt instead of Greek yogurt for a different flavor profile.
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Add Some Fun: Consider mixing in mini chocolate chips to the cheesecake batter. This adds a touch of sweetness and makes the Skinny Mini Pumpkin Cheesecakes even more enticing!
What to Serve with Skinny Mini Pumpkin Cheesecakes
The autumn-inspired flavors of these mini cheesecakes create a cozy dining experience that calls for a delightful array of pairings.
- Cinnamon-spiced Coffee: The warmth of cinnamon complements the pumpkin spice while enhancing the indulgent feel of the desserts.
- Apple Crisp: This warm, crunchy dessert echoes the fall flavors and provides a beautiful contrast to the creamy cheesecakes. Enjoy it with a scoop of vanilla ice cream.
- Roasted Brussels Sprouts: Their nutty flavor and crispy texture balance the sweetness of the cheesecakes, creating a harmonious meal.
- Fall Harvest Salad: A fresh mix of arugula, pecans, and pomegranate seeds will add brightness and a burst of flavor to the table.
- Vanilla Ice Cream: Creamy ice cream heightens the pumpkin flavor and gives the cheesecakes an extra touch of creaminess; a match made in dessert heaven!
- Salted Caramel Drizzle: A drizzle of this sticky goodness over the cheesecakes elevates their natural sweetness. A simple yet indulgent touch that brings everything together!
- Herbal Tea: A soothing cup of chamomile or peppermint tea can help cleanse the palate while allowing the rich flavors to linger.
- Chocolate-covered Pretzels: The salty crunch of pretzels wrapped in chocolate provides texture and a sweet-savory contrast that delights the senses.
- Spiced Apple Cider: Warm or cold, this classic fall drink embraces the cheerful vibes of the season, making it a delicious accompaniment.
- Pumpkin Pie: Leaning into the theme, a small slice of traditional pumpkin pie has nostalgic flavors that will charm guests and add to the festive atmosphere.
Make Ahead Options
These Skinny Mini Pumpkin Cheesecakes are perfect for busy home cooks looking to save time during the holiday season! You can prepare the pecan crust up to 24 hours in advance and keep it in the refrigerator (covered with plastic wrap) to maintain its crunchiness. Furthermore, the cheesecake filling can be mixed ahead of time and stored in the fridge for an additional 3 days. When you’re ready to serve, simply fill each crust with the chilled cheesecake batter and bake as directed. This way, you’ll enjoy all the deliciousness of your mini desserts with minimal effort, allowing you to focus on what truly matters during those festive gatherings!

Skinny Mini Pumpkin Cheesecakes Recipe FAQs
What type of pecans should I use for the crust?
You can use raw pecans for their natural crunch and flavor, but I often opt for lightly toasted pecans to heighten the nuttiness of the crust. If you’re looking for an alternative, finely chopped walnuts work beautifully too!
How should I store the cheesecakes once baked?
After they cool, store your Skinny Mini Pumpkin Cheesecakes in an airtight container in the refrigerator for up to 5-6 days. They are best enjoyed chilled, so just grab one from the fridge whenever you’re craving a treat!
Can I freeze these cheesecakes for later?
Absolutely! To freeze, place the mini cheesecakes in an airtight container or wrap them individually in plastic wrap. They can be stored in the freezer for up to 2 months. When you’re ready to enjoy one, simply thaw it overnight in the fridge for the best texture.
What if my crust feels too crumbly?
If your crust seems crumbly, it might be due to a lack of binding. Make sure you’re using sufficient butter and correctly measuring your wet ingredients. If this happens, try adding a splash more water or a bit more melted butter to reach a more manageable consistency when pressing into the liners.
Can I make these mini cheesecakes dairy-free?
Yes! For a dairy-free option, use a dairy-free cream cheese and swap the Greek yogurt for a plant-based yogurt. Just ensure that all your other ingredients are dairy-free as well, and you’ll still end up with a delicious result!
How can I make these cheesecakes sweeter?
If you prefer a sweeter treat, you can easily increase the maple syrup or honey used in the filling and the crust. Remember to taste the batter before filling the crusts—it’s the best way to ensure your medley is just right for your palate!

Skinny Mini Pumpkin Cheesecakes That Spark Fall Joy
Ingredients
Equipment
Method
- Preheat your oven to 325°F (165°C) and prepare a muffin tin with cupcake liners, spraying each with non-stick spray.
- Combine chopped pecans, maple syrup (or honey), water, and melted unsalted butter in a mixing bowl and stir until blended. Firmly press into the bottom of each cupcake liner.
- Bake the crust for 13-14 minutes until slightly browned and firm. Let cool slightly.
- In a large bowl, beat the reduced fat cream cheese until smooth. Add Greek yogurt, maple syrup (or honey), pumpkin puree, pumpkin spice, and vanilla extract. Mix until creamy, then fold in one egg.
- Spoon the cheesecake batter into the crusts, filling nearly to the top.
- Increase oven temperature to 350°F (175°C) and bake for 17-20 minutes until the center is slightly jiggly.
- Cool at room temperature for 30 minutes, then refrigerate for at least 2 hours before serving.

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