Looking for a healthier alternative to your favorite fall dessert? These Healthy Pumpkin Cheesecakes are the perfect option! With the rich, creamy texture of cheesecake but made lighter, these mini treats are a guilt-free indulgence. Made with Greek yogurt, a touch of maple syrup, and almond flour for the crust, they are gluten-free, low-fat, and just the right amount of sweet. Whether you’re prepping for a holiday gathering or craving a comforting dessert, these cheesecakes are sure to satisfy!
Table of Contents
Deliciously Healthy and Easy to Make
These Healthy Pumpkin Cheesecakes stand out because they strike the perfect balance between indulgent and nutritious. They are a healthier version of the classic cheesecake, replacing some of the cream cheese with Greek yogurt, which cuts down on fat and calories. The almond flour crust is gluten-free, and the entire dessert is naturally sweetened with maple syrup and a small amount of brown sugar. These cheesecakes are not only lower in fat but also a great option for those looking to enjoy a seasonal treat without the extra guilt.
Ingredients
For the Crust:
• Almond flour: Adds a nutty flavor and provides a gluten-free, grain-free base for the cheesecake.
• Brown sugar: Sweetens the crust just enough without overpowering the other flavors.
• Ground cinnamon: Enhances the flavor profile of the crust, giving it a warm, fall-inspired taste.
• Butter (melted): Binds the crust ingredients together while adding richness.
For the Filling:
• Neufchâtel cream cheese: A lower-fat version of cream cheese that maintains the creamy texture without the extra calories.
• Nonfat Greek yogurt: Adds creaminess and a tangy flavor while keeping the cheesecake light and packed with protein.
• Pumpkin puree: Brings the iconic autumn flavor to the cheesecake and provides nutrients like vitamin A.
• Maple syrup: A natural sweetener that complements the pumpkin flavor without being overly sweet.
• Vanilla extract: Adds a subtle sweetness and depth to the filling.
• Ground cinnamon, nutmeg, and ginger: These warm spices enhance the pumpkin flavor, creating that cozy, fall-inspired taste.
Alternative Ingredient Suggestions
If you don’t have almond flour on hand, you can easily swap it out for graham crackers, making sure to adjust the sugar level. For those with a nut allergy, graham crackers are an excellent option for the crust. If you prefer a different sweetener, honey can be used in place of maple syrup, though maple syrup gives a distinct autumn flavor that pairs wonderfully with pumpkin.
Step-by-Step Instructions
- Preheat the oven to 350°F (175°C).
- In a mixing bowl, combine the almond flour, brown sugar, cinnamon, and melted butter. Stir until the mixture reaches a coarse, sand-like texture.
- Line a 12-cup muffin tin with foil or silicone muffin liners. Press about 1.5 tablespoons of the crust mixture into each cup.
- Bake the crusts for 11-12 minutes, or until the edges begin to turn golden brown. Let them cool while you prepare the filling.
- In a stand mixer or with a hand mixer, whip together the Neufchâtel cream cheese, Greek yogurt, pumpkin puree, maple syrup, vanilla extract, and the spices. Mix for 5-6 minutes until smooth and fully combined.
- Once the crusts have cooled, spoon about 3 tablespoons of the filling into each muffin cup, filling them about three-quarters of the way.
- Place the cheesecakes in the refrigerator to chill for at least 6-8 hours or overnight for the best texture.

Tips & Tricks
- For the smoothest filling, ensure that the cream cheese and yogurt are at room temperature before mixing. Cold ingredients can result in a lumpy texture.
- These cheesecakes must be served chilled to maintain their creamy texture.
- If you’re not using silicone muffin liners, be sure to use foil liners, as paper liners may cause the cheesecakes to stick.
- To avoid a soggy crust, make sure the crust cools completely before adding the filling.
Pairing Ideas and Variations
These Healthy Pumpkin Cheesecakes are delicious on their own, but you can elevate them with various toppings and pairings. A sprinkle of cinnamon or a drizzle of homemade caramel sauce would complement the pumpkin flavor beautifully. If you’re looking for a chocolatey twist, try adding mini chocolate chips to the filling or topping them with chocolate sauce.
For a fun variation, you could try a deconstructed version by serving the filling as a creamy pumpkin mousse. These cheesecakes also make an excellent base for various garnishes like crushed nuts, whipped cream, or even a dollop of peanut butter.
These treats are perfect for the holiday season, and they store well in the refrigerator for up to 5 days. You can also freeze them for later enjoyment. Simply thaw them in the fridge for 3-4 hours before serving, or heat them in the microwave for a quick 10-15 seconds to restore their creamy texture.
Seasonal Appeal and Health Benefits
Healthy Pumpkin Cheesecakes are the ultimate fall treat, offering the rich flavor of pumpkin and spices while remaining lower in calories and fat. They are an excellent source of protein, thanks to the Greek yogurt, and packed with essential vitamins like vitamin A from the pumpkin puree. With their seasonal flavor and health-conscious ingredients, these cheesecakes are the perfect dessert to enjoy during the fall months without compromising on flavor or nutrition.
These mini cheesecakes are not only a healthier option but also easy to make and customize, making them ideal for both everyday indulgence and special occasions.
Conclusion
These Healthy Pumpkin Cheesecakes are the perfect balance of delicious and nutritious. With their creamy, indulgent filling and crispy, gluten-free crust, they are an irresistible seasonal treat that satisfies your pumpkin cravings without all the guilt. Whether you’re preparing them for a holiday gathering or a cozy night in, these mini cheesecakes will delight your taste buds while keeping your health goals in check. Easy to make, customizable, and full of autumn flavor, they’re the ideal dessert for anyone looking to enjoy the best of fall in a healthy way.
FAQs
Can I make these Healthy Pumpkin Cheesecakes ahead of time?
Yes, these cheesecakes are best when made in advance. You can prepare them 24 hours before serving to allow the flavors to fully develop and the filling to firm up. Just be sure to keep them in the fridge and let them chill for at least 6-8 hours or overnight for the best texture.
Can I use regular cream cheese instead of Neufchâtel cream cheese?
While Neufchâtel cream cheese is recommended for a lower-fat option, regular cream cheese will work just fine. Just be mindful that it may increase the fat content slightly, but it will still provide that rich, creamy texture you love.
Can I substitute the almond flour with something else?
Yes, you can swap the almond flour for finely ground graham crackers if you prefer. However, be sure to adjust the sugar content if you go this route, as graham crackers are already sweetened. For nut-free alternatives, graham crackers are a great option!
How should I store Healthy Pumpkin Cheesecakes?
These cheesecakes should be stored in an airtight container in the refrigerator for up to 5 days. If you’d like to freeze them, simply place them in a freezer-safe container and freeze for up to 2 months. To enjoy, thaw in the fridge for a few hours or microwave for a few seconds.
More Relevant Recipes
- Pumpkin Dip: 5-Ingredient Autumn Treat: This easy, creamy pumpkin dip is a perfect autumn snack that pairs well with crackers, apples, or even veggies. Simple to make and full of seasonal flavor, it complements the rich, comforting taste of pumpkin cheesecakes while offering a lighter, dip-able option for gatherings.
- Pumpkin Cheesecake Bars Recipe: A great twist on the classic cheesecake, these pumpkin cheesecake bars are creamy, flavorful, and easy to serve. With a slightly thicker crust and a perfectly spiced filling, they provide the same pumpkin cheesecake indulgence in a convenient bar format.
- Creamy Pumpkin Gnocchi Recipe: For a savory twist on the pumpkin theme, this creamy pumpkin gnocchi combines soft, pillowy gnocchi with a rich pumpkin sauce, creating a comforting, seasonal dish that’s both satisfying and unique, much like the delicious, spiced flavors of pumpkin cheesecakes.

Healthy Pumpkin Cheesecakes
- Total Time: 6 hours 22 minutes
- Yield: 12 mini cheesecakes
- Diet: Gluten Free
Description
These Healthy Pumpkin Cheesecakes are a delicious and guilt-free fall treat, made with Greek yogurt, almond flour, and a variety of warm spices. They offer a creamy texture and a rich pumpkin flavor, perfect for satisfying your seasonal cravings while keeping things lighter and healthier. These mini cheesecakes are gluten-free, low-fat, and naturally sweetened with maple syrup.
Ingredients
- 1 cup almond flour
- 1/4 cup brown sugar, loosely packed
- 1/2 teaspoon ground cinnamon
- 4 tablespoons butter, melted
- 8 ounces Neufchâtel cream cheese (⅓ less fat)
- 2/3 cup nonfat Greek yogurt
- 1/2 cup pumpkin puree
- 3 tablespoons maple syrup
- 2 teaspoons vanilla extract
- 3/4 teaspoon ground cinnamon
- 1/4 teaspoon ground nutmeg
- 1/4 teaspoon ground ginger
Instructions
- Preheat oven to 350°F (175°C).
- In a mixing bowl, combine almond flour, brown sugar, cinnamon, and melted butter. Stir until the mixture resembles a coarse sand texture.
- Line a 12-cup muffin tin with foil or silicone muffin liners.
- Press about 1.5 tablespoons of the crust mixture into each muffin cup and bake for 11-12 minutes, until the edges start to brown.
- Allow the crusts to cool while preparing the filling.
- In a stand mixer or using a hand mixer, beat together Neufchâtel cream cheese, Greek yogurt, pumpkin puree, maple syrup, vanilla extract, cinnamon, nutmeg, and ginger. Mix on high for 5-6 minutes until smooth and fully combined.
- Spoon 3 tablespoons of the filling into each muffin cup, filling them ¾ of the way full.
- Place the cheesecakes in the fridge to chill for 6-8 hours or overnight for the best texture.
Notes
- Ensure cream cheese and yogurt are at room temperature for a smoother filling.
- Use silicone or foil muffin liners to prevent sticking; avoid paper liners.
- If using graham crackers instead of almond flour, reduce the amount of brown sugar to prevent the crust from being too sweet.
- For a dairy-free option, Neufchâtel cream cheese can be replaced with a non-dairy alternative (though not recommended for the best texture).
- Chill the cheesecakes for at least 6 hours, but preferably overnight, for the best texture and flavor.
- Prep Time: 10 minutes
- Cook Time: 12 minutes
- Category: Dessert
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 mini cheesecake
- Calories: 168 kcal
- Sugar: 10g
- Sodium: 128mg
- Fat: 11g
- Saturated Fat: 4g
- Unsaturated Fat: 7g
- Trans Fat: 0g
- Carbohydrates: 13g
- Fiber: 1g
- Protein: 5g
- Cholesterol: 21mg