Healthy Pumpkin Cheesecakes Recipe
If you’re looking for a delightful treat that offers all the creamy goodness of cheesecake with a seasonal twist, these Healthy Pumpkin Cheesecakes will quickly become your new favorite. Each mini cheesecake boasts a luscious filling packed with warming spices and velvety pumpkin, all nestled on a perfectly spiced almond flour crust. What’s truly wonderful about this recipe is how it masterfully balances indulgence with wholesome ingredients, making every bite feel like a cozy hug that’s actually good for you.

Ingredients You’ll Need
Every ingredient in these Healthy Pumpkin Cheesecakes is carefully chosen to create the perfect harmony of flavors and textures. From the nutty almond flour crust that adds a satisfying crunch to the silky pumpkin-spiced filling that melts in your mouth, each element plays a key role in making this dessert irresistible yet wholesome.
- 1 cup almond flour: Provides a naturally gluten-free, buttery base with a subtle nuttiness that complements the pumpkin beautifully.
- 1/4 cup brown sugar: Adds just the right touch of sweetness and helps the crust caramelize slightly during baking.
- 1/2 teaspoon ground cinnamon: Infuses the crust with warm, aromatic spice essential for that fall flavor profile.
- 4 tablespoons butter, melted: Binds the crust ingredients and adds richness for a tender yet sturdy base.
- 8 ounces Neufchatel cream cheese (⅓ less fat): Keeps the cheesecake creamy while cutting calories and fat for a lighter option.
- 2/3 cup nonfat Greek yogurt: Brings tanginess and boosts protein, plus it helps achieve that smooth, airy filling texture.
- 1/2 cup pumpkin puree: The star ingredient delivering natural sweetness, vibrant color, and all those pumpkin nutrients.
- 3 tablespoons maple syrup: Adds gentle sweetness with a hint of caramel complexity—perfect for this autumn dessert.
- 2 teaspoons vanilla extract: Enhances all the flavors and adds a lovely fragrant depth.
- 3/4 teaspoon ground cinnamon: More warm spice magic inside the filling for that comforting pumpkin pie taste.
- 1/4 teaspoon ground nutmeg: Provides subtle heat and nutty notes balancing the sweetness.
- 1/4 teaspoon ground ginger: Brings a tiny zing that brightens and rounds out the spices.
How to Make Healthy Pumpkin Cheesecakes
Step 1: Prepare the Crust
Start by mixing the almond flour, brown sugar, and cinnamon together until combined. Then pour in the melted butter and gently stir until everything resembles coarse sand. Press this mixture firmly into the bottoms of your muffin liners, ensuring an even layer in all 12 cups. Bake at 350 degrees Fahrenheit for 11-12 minutes until the crust edges just start to turn golden brown, creating a firm, crunchy base that will hold the luscious filling perfectly.
Step 2: Make the Filling
While your crusts cool, bring all filling ingredients to room temperature for the best blend. In a stand mixer or with a hand mixer, whip the Neufchatel cream cheese, Greek yogurt, pumpkin puree, maple syrup, vanilla, and spices on high speed for 5-6 minutes. This thorough mixing ensures a luxuriously smooth and airy filling that’s free of lumps, giving your cheesecakes a professional texture that’s hard not to love.
Step 3: Assemble and Chill
Once the crusts have cooled completely, spoon about 3 tablespoons of the pumpkin filling into each muffin cup. The filling should reach roughly three-quarters full, leaving a little room to avoid overflow when chilling. Place the tray in the fridge for at least 6-8 hours, or preferably overnight. This chilling time allows the cheesecakes to set firmly while the flavors meld wonderfully, yielding a rich yet healthy dessert ready to impress.
How to Serve Healthy Pumpkin Cheesecakes

Garnishes
Add an extra layer of texture and flavor by topping the cheesecakes with a sprinkle of toasted pecans, a dusting of cinnamon, or a small dollop of light whipped cream. A drizzle of pure maple syrup or a few fresh cranberries can also brighten up the presentation and perfectly complement the warm spices inside.
Side Dishes
For a festive dessert spread, pair these healthy pumpkin cheesecakes with a hot cup of chai tea or spiced coffee. They also shine alongside fresh fruit salad or a simple bowl of mixed berries, which add a refreshing contrast and make your indulgence feel balanced and well-rounded.
Creative Ways to Present
If you’re hosting a party, these mini cheesecakes are perfect for individual servings—no slicing required. Place each cheesecake in a decorative paper liner topped with a cinnamon stick or mini pumpkin, or serve on small plates with a garnish of edible flowers for a stunning seasonal effect that will wow your guests.
Make Ahead and Storage
Storing Leftovers
Leftover Healthy Pumpkin Cheesecakes keep beautifully refrigerated in an airtight container for up to 4 days. This makes them a fantastic make-ahead dessert or snack that you can enjoy throughout the week without any loss of flavor or texture.
Freezing
You can freeze these cheesecakes for up to 2 months. Wrap each cheesecake individually in plastic wrap before placing them in a freezer-safe container to prevent freezer burn and preserve freshness. When ready to eat, thaw them overnight in the fridge for best results.
Reheating
These cheesecakes are best enjoyed chilled, but if you prefer a slightly softer texture, allow them to sit at room temperature for about 10-15 minutes before serving. Avoid microwaving as it may alter the smooth texture and cause separation.
FAQs
Can I use regular cream cheese instead of Neufchatel?
Yes, you can use regular cream cheese, but Neufchatel has less fat and makes this recipe lighter without sacrificing flavor. It’s a great option when aiming for healthy pumpkin cheesecakes.
Is it necessary to chill the cheesecakes overnight?
While chilling for 6-8 hours is sufficient, overnight chilling helps the flavors meld and ensures the filling is completely set for that perfect creamy texture.
Can I make these gluten-free?
Absolutely! The recipe uses almond flour for the crust, which is naturally gluten-free, making these cheesecakes a perfect treat for those avoiding gluten.
What can I substitute for maple syrup?
If you don’t have maple syrup, you can use honey or agave nectar as alternatives, but they might slightly change the flavor profile. Brown rice syrup is another good option for a milder sweetness.
Can I add nuts inside the filling?
Yes, finely chopped nuts like pecans or walnuts can be folded into the filling for added texture and a nutty boost. Just be careful not to overpower the smooth, creamy characteristic of the cheesecake.
Final Thoughts
These Healthy Pumpkin Cheesecakes are such a joy to make and even more delightful to eat. The ease of preparation combined with the wonderfully balanced flavors makes this recipe a must-try, especially when you want a dessert that feels indulgent but keeps things wholesome. So grab your ingredients, invite some friends over, and share the love baked into every bite of these cozy little treats!
PrintHealthy Pumpkin Cheesecakes Recipe
These Healthy Pumpkin Cheesecakes are a guilt-free twist on the classic dessert, featuring a low-fat crust made with almond flour and a creamy, spiced pumpkin filling enhanced with greek yogurt and natural sweeteners. Perfect for a nutritious treat during the fall or any time you crave a smooth, flavorful cheesecake without the heaviness.
- Prep Time: 20 minutes
- Cook Time: 12 minutes
- Total Time: 8 hours 32 minutes
- Yield: 12 mini cheesecakes 1x
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Ingredients
Crust
- 1 cup almond flour
- 1/4 cup brown sugar, loosely packed
- 1/2 teaspoon ground cinnamon
- 4 tablespoons butter, melted
Filling
- 8 ounces Neufchatel cream cheese (⅓ less fat cream cheese), room temperature
- 2/3 cup nonfat Greek yogurt, room temperature
- 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
- Prepare Ingredients: Bring all filling ingredients to room temperature to ensure a smooth, creamy cheesecake filling without lumps.
- Preheat Oven: Set your oven to 350°F (175°C) to preheat for baking the crust.
- Make Crust Mixture: Stir together almond flour, brown sugar, and ground cinnamon until evenly combined with a coarse sand-like texture. Add the melted butter and mix well.
- Line Muffin Pan: Use foil or silicone muffin liners in a 12-cup muffin pan to prevent sticking.
- Form Crusts: Press about 1.5 tablespoons of the crust mixture into the bottom of each muffin cup, distributing any leftover crust mixture evenly across all cups.
- Bake Crust: Bake the crusts for 11-12 minutes at 350°F until edges begin to turn a light golden brown.
- Cool Crust: Remove the muffin pan from the oven and let crusts cool completely, placing them in the refrigerator if you want to speed up the process.
- Prepare Filling: In a stand mixer bowl or with a hand mixer, combine the Neufchatel cream cheese, nonfat Greek yogurt, pumpkin puree, maple syrup, vanilla extract, and spices. Whip on high speed for 5-6 minutes until smooth and fully incorporated.
- Fill Cheesecakes: Once the crusts are cool, spoon about 3 tablespoons of the filling into each muffin cup, filling them approximately ¾ of the way full.
- Chill Cheesecakes: Refrigerate the mini cheesecakes for 6-8 hours or overnight to allow them to set properly.
Notes
- Bringing the cream cheese and yogurt to room temperature is essential for a smooth filling texture.
- Use silicone or foil liners to make removal of cheesecakes easier and to avoid sticking.
- You can substitute maple syrup with honey or agave nectar if preferred.
- For a dairy-free variation, consider using vegan cream cheese and yogurt alternatives, though texture may vary.
- Store cheesecakes covered in the refrigerator and consume within 3-4 days for best freshness.
Nutrition
- Serving Size: 1 mini cheesecake
- Calories: 150 kcal
- Sugar: 6 g
- Sodium: 90 mg
- Fat: 9 g
- Saturated Fat: 3.5 g
- Unsaturated Fat: 5 g
- Trans Fat: 0 g
- Carbohydrates: 12 g
- Fiber: 2 g
- Protein: 5 g
- Cholesterol: 22 mg
Keywords: healthy pumpkin cheesecake, low fat cheesecake, mini cheesecakes, pumpkin dessert, fall dessert, sugar conscious dessert