Easy Mini Lemon Cheesecakes are the perfect dessert! Made with only 8 ingredients – these healthy cheesecakes are simple and yummy!

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If you’re looking for an easy, delicious dessert – these Mini Lemon Cheesecakes are the best!
A buttery cookie crust gets layered with rich, creamy lemon filling. The best part about it is that they’re secretly healthy (I promise no one will know!)
This recipe uses good for you ingredients like an almond flour base and 1/3 less fat cream cheese to create a rich, decadent treat that’s just as delicious as the ‘real’ thing.

why we love this healthy dessert
What’s not to love about mini lemon cheesecakes? These treats are light and bursting with flavor while having the perfect amount of rich, creaminess. Here’s why we love this recipe:
- Easy to make: These cheesecakes only are made with a few ingredients. They only take about 20 minutes of work to make (the rest of the time is for baking/chilling!)
- Gluten Free: These mini cheesecakes are gluten free which means everyone can enjoy them!
- Delicious: Above everything, these cheesecakes are SO yummy. They’re the perfect spring dessert!
Ingredients for Mini Lemon Cheesecakes
To make mini lemon cheesecakes you’ll need:
- Bob’s Red Mill Almond Flour
- brown sugar
- cinnamon
- butter
- Neufchâtel cream cheese
- nonfat greek yogurt
- honey
- lemon zest/lemon juice
- lemon extract
A citrus juicer and citrus zester will also be helpful to have! We also used silicone muffin liners.
You can find substitutions for all of these ingredients below in the green shaded substitutions box.

We used Bob’s Red Mill Almond Flour for the base of the cheesecakes. We love baking with Bob’s, especially around the holidays! Whether it’s using their all purpose flour in our Italian Cream Pie, or taking a shortcut and using their baking mixes in Brownie Truffles – our pantry is always stocked with their goods!
Almond flour is great for making recipes gluten free and lower carb which is why we chose it for this recipe!
How to Make Healthy Lemon Cheesecake
Making mini lemon cheesecakes couldn’t be easier! Here’s how to make them.
- Mix together the crust. Press 1.5 tablespoons of the crust mix into each of the 12 muffin cups. Make sure to cover the entire bottom of all the cups and gently press the filling down.
- Bake the crust for 13-14 minutes at 350 until the edges start to brown a tiny bit.
- Once the crusts have cooked, remove the crusts from the oven and allow the crusts to cool while you prepare the filling.
- In the bowl of a stand mixer or with a hand mixer- use your whisk attachment and whip together cream cheese, greek yogurt, honey, lemon zest/juice and lemon extract on high speed for 5-6 minutes until smooth.
- When your crust is completely cool, scoop 3 tablespoons of cheesecake filling into each of the muffin cups, filling ¾ of the way.
- Put the cheesecakes into the fridge and chill for 6-8 hours or overnight. You can also put the cheesecakes in the freezer for 2-3 hours if you’d like them to set quicker.
- Store the cheesecakes for up to 5 days in the refrigerator.





SUBSTITUTIONS FOR HEALTHY LEMON CHEESECAKES
Almond Flour: You can sub in 1 cup of finely ground graham crackers for almond flour. If you do this, we recommend skipping the brown sugar or cutting it in half. You can’t substitute coconut flour for almond flour. It doesn’t work with the cream cheese. The almond flour crumb mimics the graham crackers best.
Butter: I haven’t tried substituting butter in this recipe. Melted coconut oil or olive oil might work but I can’t be sure. I wouldn’t recommend it.
Sugar: We tried a honey infused crust to really try to mimic the classic graham cracker crust flavor but it just didn’t pop through. We also tried one with coconut sugar and did not like the taste. Brown sugar is the best choice here. It’s a ¼ cup over 10 mini cheesecakes which I think is a good ratio.
Neufchâtel Cream Cheese: Neufchâtel Cream Cheese is just lower fat cream cheese. We use the cream cheese in a block (not whipped versions) I haven’t used regular cream cheese in this recipe, but I think it would work. It would make the cheesecakes higher in fat/calories.
Greek Yogurt: I have not tried substituting the greek yogurt in this recipe. Full fat yogurt may work but I can’t be sure.
Dairy Free: We do not recommend any dairy free options for this recipe.
Room Temperature: It is very important that these ingredients are brought to room temperature for the smoothest filling. If you don’t, your filing won’t be as smooth. Cream cheese will leave little lumps if it’s not completely to room temp. This will still be fine for eating it, but not necessarily for presentation. I think a fresh fruit garnish would be great with the “cookie” crumbs.
Baked: We don’t recommend baking these cheesecakes. In order to get a nice looking cheesecake with the yogurt, you’d need to have a water bath in the oven and it’s overall a lot of work!
Muffin Liners Foil or silicone muffin liners work best. Paper ones risk sticking and taking on too much moisture. (You will be using 12 liners because 2 of these crusts are going to be garnish crusts for the top of your cheesecakes. This is optional, but recommended!)
Mix ins: I haven’t tried mixing anything into the filling of this (peanut butter, chocolate, berries, etc) but I think it would work. Alternatively, you can just top the cheesecakes with whatever garnish you like. We have a recipe for Healthy Pumpkin Cheesecakes that is delicious if you’re looking for a flavored cheesecake or Healthy Cheesecake Bites that are plain.
Making one large cheesecake: I haven’t tried making one large cheesecake with this recipe but I think it would work if you were to make it in a springform cheesecake pan
To Make it Lower Carb: You can try using a no carb/low carb sweetener but I have not tested this so I can’t be sure how it would work.

How to Serve Healthy Lemon Cheesecakes
These yummy lemon cheesecakes are best made 24 hours in advance of when you have to serve them. They only need about 6 hours to chill, but if they can set in the refrigerator overnight they’ll be even better!
Serve cold: These cheesecakes should be served cold. They’re fine to sit out at room temp for 1-2 hours, but they will get soft, and they’re meant to be eaten cold.
With berries: We served these with lemon wedges and fresh berries on top, but you can serve them however you like!
How to Store Healthy Cheesecakes
Refrigerator: These mini lemon cheesecakes must be stored in the refrigerator. They will last in the refrigerator for up to 5 days. They can get a little moist on top from condensation in the refrigerator so I recommend just blotting them with a paper towel before serving if that happens
Freezing: These cheesecakes freeze very well. When ready to eat -remove and defrost for 10-15 minutes at room temperature. They will last in the freezer for up to a month

Other healthy dessert recipes:
Here are some of our favorite easy, healthy desserts!

Mini Lemon Cheesecakes
Ingredients
Crust
- 1 cup Bob’s Red Mill Almond Flour
- ¼ cup brown sugar
- ½ teaspoon cinnamon
- 4 tablespoons butter melted
Cheesecake Filling
- 8 ounces Neufchâtel cream cheese or low fat cream cheese
- ¾ cup 0% nonfat greek yogurt 6 ounces
- ¼ cup honey
- 1 tablespoon lemon zest
- 1 tablespoon lemon juice
- 1 teaspoon lemon extract
Instructions
- Note: It is important that these ingredients are brought to room temperature for the smoothest filling. If you don’t, your filing won’t be as smooth and will have bumps in it.
- Preheat the oven to 350 degrees.
- To make the crust, stir together almond flour, brown sugar, cinnamon and melted butter until a coarse sand-like texture forms. Line a 12 cup muffin tin silicone muffin liners. (Foil liners will also work. Do not bake without liners)
- Press 1.5 tablespoons of the crust mix into each of the 12 muffin cups. If you have extra crust, evenly distribute it among the muffin tin. Make sure to cover the entire bottom of all the cups and gently press the filling down.
- Bake the crust for 13-14 minutes at 350 until the edges start to brown a tiny bit.
- Once the crusts have cooked, remove the crusts from the oven and allow the crusts to cool while you prepare the filling.
- In the bowl of a stand mixer or with a hand mixer- use your whisk attachment and whip together cream cheese, greek yogurt, honey, lemon zest/juice and lemon extract on high speed for 5-6 minutes until smooth.
- When your crust is completely cool, scoop 3 tablespoons of cheesecake filling into each of the muffin cups, filling ¾ of the way.
- Put the cheesecakes into the fridge and chill for 6-8 hours or overnight. You can also put the cheesecakes in the freezer for 2-3 hours if you’d like them to set quicker.
- Store the cheesecakes for up to 5 days in the refrigerator.
Lauren says
I made these following the recipe exactly as written, I just used a silicone cupcake baking pan instead of liners bc I didn’t feel like washing all the liners. They pop out better if put in the freezer an hour or so before serving, but they did pop out after refrigerated too just not as easily. Love bright lemon flavors, my family liked them too!! My cousin was shocked that her gluten free self could eat them bc honestly we usually don’t make gluten free desserts bc she’s the only one. No one could tell they were GF and she was thankful.
Ashley says
These were so yummy!
Berni says
If I could give these 10 or 100 stars I would! I had to postpone making this recipe and I probably should have continue to put it off. I was worried I would eat them all and I ate all but 2 (whoops, haha). These are dangerous…so good and refreshing especially in this 108 degree Texas heat.