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Gluten-Free Mini Cheesecakes

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These mini cheesecakes are a creamy confection, sweetened with just honey and maple syrup and guaranteed to be the hit of the party! Ground flax seeds give the crust a delicious nutty flavor making these clean eating cheesecakes absolutely crave-worthy!

a mini cheesecake with blueberries and a mint leaf on top of a white plate with pink purees

Cheesecake is my all-time favorite dessert, but it is packed with white sugar. This year I made it my mission to come up with a cheesecake recipe that didn’t use white sugar. This recipe was the result.

Not only is it delicious, but it isn’t as sweet as traditional cheesecakes, so it doesn’t leave you with a heavy, full feeling!

Clean Eating Cheesecake Crust Recipe

a picture of all the ingredients needed to make the crust

What you need to make cheesecake crust:

  • Almond Flour – The almond flour replaces the traditional wheat flour and/or graham crackers in cheesecake crust.
  • Ground Flax – The flax adds a delicious nutty flavor to the crust. Since we aren’t using graham crackers, this adds a complex flavor that is so delicious!
  • Butter – Use a good grassfed butter like Kerrygold to keep this clean. It also just tastes better!
  • Honey – The honey is optional. The crust is still delicious without the honey
  • Salt

Using a pastry cutter, cut the butter into the dry ingredients until it resembles coarse sand. Make sure the butter is very cold or the crust may melt in the oven.

If you prefer, you can use a food processor in place of the pastry cutter. Pulse the ingredients until the butter is incorporated.

two pictures - one with all the crust ingredients mixed together and the second with the crust in a blue silicone muffin pan

Press the crust mixture into a cupcake pan. This recipe will make 12 mini cheesecakes.

Bake at 325° for 15 minutes or until it is just starting to brown.

How to Make Cheesecake – Clean Eating Version

a picture of all the ingredients needed to make the cheesecake

What you will need:

  • Cream Cheese – Is cream cheese clean? It depends on who you ask. Cream cheese is still slightly processed, but it is considered clean by some. I do not include it in my regular clean diet, but in this case, it is needed to make a comparable cheesecake. This is a case of making an exception to stay away from the sugar-laden cheesecakes!
  • Honey and Maple Syrup – We use a blend of the two to get a sweet flavor without changing the taste of the cheesecake
  • Eggs – The eggs are needed to stabilize the cheesecake and make it firm
  • Cornstarch– The maple syrup and honey add liquid to the batter, so we countered it by adding just a touch of cornstarch
  • Lemon zest– Completely optional, but it adds a delicious dimension to the cheesecake!

Tips For Making Cheesecake

a side view of the mini crusts without toppings. You can see the layer ofcrust and the cheesecake on top
  • How to tell if cheesecake is done? Gently shake the pan to see if the middle is jiggly but the outer edges are cooked, it is done. About 1/4 inch around the edges should be cooked. The middle will continue to cook while it cools and will be perfect!
  • How to prevent cracks in cheesecake? To be honest, I haven’t perfected this. Instead, I don’t worry about the cracks and I just cover it up with toppings. If you are concerned about cracks, it has to do with how quickly the cheesecake cools. You can leave it in the oven to cool and remove it only after it is at room temperature. In addition, you can use a water bath
  • Does this recipe use a water bath? No, I learned early on that it is possible to make a cheesecake without a water bath, so this recipe does not use one. Again, it cracked tops bother you, you will want to go with a water bath recipe.

Cheesecake Toppings

There are so many options when it comes to toppings. In these photos, I used a simple Berry Puree. I followed THIS recipe but did not strain the seeds. In this dish, the seeds don’t affect the flavor.

Also, try it with a whipped coconut whipped cream. Add nuts, berries, purees and even hemp hearts!

These mini cheesecakes were a hit with the kids and I will be making them all summer long! Try them today and let me know what you think!

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Mini Cheesecakes

Mini Cheesecakes

Yield: 12 Cheesecakes
Prep Time: 30 minutes
Cook Time: 1 hour 15 minutes
Additional Time: 3 hours
Total Time: 4 hours 45 minutes

These mini cheesecakes are a creamy confection, sweetened with just honey and maple syrup and guaranteed to be the hit of the party! Ground flax seeds give the crust a delicious nutty flavor making these clean eating cheesecakes absolutely crave-worthy!


Cheesecake Crust

  • 1 Cup Almond Flour
  • 1/4 Cup Flax Seeds, Ground
  • 4 Tablespoons Butter
  • 1 Tablespoon Honey
  • 1/4 teaspoon Salt

Cheesecake Filling

  • 16oz Cream Cheese
  • 2 Eggs
  • 1/4 Cup Honey
  • 1/4 Cup Maple Syrup
  • 1 Tablespoon Cornstarch
  • 1 teaspoon Vanilla
  • 1 teaspoon Lemon Zest


Cheesecake Crust

  1. Preheat oven to 325°
  2. Add the Almond Flour, Flax seeds, Butter, Honey and Salt to a medium bowl.
  3. Use a pastry cutter to cut the butter into the dry ingredients. It is done when the dough resembles coarse sand and holds together when pinched
  4. Press the crust into a 12-count muffin pan
  5. Bake at 325° for 15 minutes or until the crust just starts to brown

Cheesecake Filling

  1. In a medium bowl, add the Cream Cheese, Eggs, Honey, Maple Syrup, Vanilla and Cornstarch.
  2. Use a hand blender to blend until smooth.
  3. Mix in the lemon zest
  4. Evenly divide the mixture among the 12 muffin cups. There may be extra filling that can be baked in a separate pan.
  5. Bake for 35 minutes. The middle should still be jiggly when the pan is shaken. The middle will set as it cools.
  6. Let cool for 3 hours then place in the fridge overnight. Top as desired and enjoy!
Nutrition Information:
Yield: 12 Serving Size: 1
Amount Per Serving: Calories: 299Total Fat: 24gSaturated Fat: 11gTrans Fat: 0gUnsaturated Fat: 11gCholesterol: 79mgSodium: 207mgCarbohydrates: 18gFiber: 2gSugar: 13gProtein: 6g

Nutritional information was calculated automatically. Please verify accuracy

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By on June 26th, 2020

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2 thoughts on “Gluten-Free Mini Cheesecakes”

  1. So delicious! My niece gluten intolerant and she is having a wedding soon. EEK. I had no idea what to serve at her shower until I saw these cute little cheesecakes. I love the almond flour crust and am going to use it in a lot of my other recipes.


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