Healthy Cheesecake Bites are the perfect low fat cheesecake treat! Made with greek yogurt, low in sugar and so delicious! Gluten and grain free – this is one of our favorite lighter desserts! This post is sponsored by FAGE; however, all thoughts and opinions are my own.

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I didn’t think I could love cheesecake more.. and then these lightened up greek yogurt cheesecake came along.
Hello new favorite dessert!
These healthy cheesecake bites are the perfect treat. They’re rich and creamy while having a perfectly sweet cookie crust. Top with fresh berries and they’re not only delicious – but adorable!
These cheesecakes are also SUPER easy to make. You only need 8 simple ingredients to make them!
What makes these cheesecakes better for you?
These cheesecakes are a lightened up version of the classic dessert you know and love.
- Lower in fat – A slice of cheesecake typically has about 30-40g of fat. These mini cheesecakes have 15g of fat per serving, which is almost half! The rich creaminess of FAGE Total 0% Greek yogurt helps to replace some of the cream cheese and make these much lighter.
- Gluten/Grain Free- Cheesecake is often made with graham cracker crust – this recipe has almond flour for the base for all my gluten/grain free friends!
- Lower in sugar – Most cheesecakes have over 30g of sugar per slice. This recipe only has 14g of sugar. The filling is sweetened with honey and there’s a tiny bit of brown sugar in the crust.

Ingredients for Lower Fat Cheesecake
To make these mini healthier cheesecakes you’ll need:
- almond flour
- neufchatel cream cheese
- Greek Yogurt
- vanilla extract
- brown sugar
- cinnamon
- honey
- melted butter
The FAGE Total 0% Yogurt is what gives these cheesecakes a rich texture while keeping them lower in fat than most cheesecakes!

You’ll also need a muffin tin and silicone muffin liners.
We like these silicone muffin liners the best because the cheesecakes pop right out of them. Foil liners will also work, but paper liners won’t as they will get stuck.
You can find substitutions for all of these ingredients below in the green shaded box.
How to make Healthier Cheesecake
It’s so simple to make these mini cheesecake bites! To make healthier cheesecakes:
- Mix together your crust.
- Once your crust has combined, press into silicone muffin liners and bake until golden brown.
- As crusts are baking – whip together filling until it is smooth and creamy.
- Scoop the filling into the baked crusts.
- Place in the refrigerator for 6-8 hours until chilled.
- When the cheesecakes have chilled, add fresh berries on top and serve.





Substitutions for Healthy cheesecakes:
We have included a few suggestions for this recipe below for you.
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!
Coconut Flour: 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.
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.
Nut Free/ Graham Crackers: You can easily sub in 1 cup of finely ground graham crackers for almond flour. If you do this, we recommend taking out the brown sugar since those are sweet. I’d still add in the cinnamon if they are honey graham crackers.
Dairy Free: We do not recommend any dairy free options for this recipe.
Neufchâtel Cream Cheese: This is just cream cheese with 1/3 less fat. Make sure to use the one in the block. Do not use any whipped versions. While I haven’t tested regular cream cheese in this recipe, I think it would 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 recipes for Healthy Pumpkin Cheesecakes, Key Lime Cheesecakes, and Lemon Cheesecakes that are delicious if you’re looking for a flavored cheesecake or these Mango Cheesecake Bites are delicious too!
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 spring form cheesecake pan

Serving Gluten Free Yogurt Cheesecake:
These cheesecakes are best made 24 hours in advance of when you have to serve them. They only need about 6 hours to cool, but if they can set in the refrigerator overnight they’ll be even better!
Serve chilled: These cheesecakes should be served chilled. 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 fresh berries on top, but you could also do chocolate, peanut butter, really anything you like!

How to store healthy cheesecakes:
Refrigerator: Cheesecake bites 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 – I haven’t tried freezing these cheesecakes but I wouldn’t recommend it. I don’t think they would freeze well.

Other healthy dessert recipes we love:

Healthy Cheesecake Bites
Ingredients
Crust
- 1 cup almond flour
- ¼ cup brown sugar
- ½ teaspoon cinnamon
- 4 tablespoons butter melted
Filling
- 8 ounces Neufchâtel cream cheese ⅓ less fat cream cheese
- ¾ cup 0% non fat greek yogurt (6 ounces)
- ¼ cup honey
- 2 teaspoon vanilla extract
Instructions
- Note: 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.
- Preheat oven to 350 degrees.
- Stir together all crust ingredients until a coarse sand-like texture forms. Line a 12 cup muffin pan with foil or silicone muffin liners.
- Press about 1.5 tablespoons of the crust mix into each of the 12 muffin cups. Depending on how fine your almond flour was, you might have some left over.Just distribute it evenly and cover the entire bottom of all the cups.
- Bake for 13-14 minutes at 350 until the edges start to brown a tiny bit.
- Remove crusts from the oven and allow the crust to cool while you prepare the filling.
- In the bowl of a stand mixer or with a hand mixer- use your whisk attachment (if available otherwise regular beaters are fine) and whip the mixture on high speed for 5-6 minutes until everything is incorporated.
- When your crust is completely cool, scoop 3 tablespoons of filling into each of the muffin cups.
- You will be able to fill 10 of the cups ¾ of the way. Take the other 2 crusts, remove from the pan, crumble them up and set aside for garnishment.
- Put the cheesecakes into the fridge and chill for 6-8 hours or overnight.
Berni Shalda says
These were so easy to make and taste was amazing. I may or may not have licked the bowl clean. Super quick as well. I put the crusts in the fridge to help cool them down faster because I am an impatient baker. I also may or may not share!
The Clean Eating Couple says
So glad you enjoyed the, Berni! Thank you so much!
Ashley Orfitelli says
So easy & so delicious! Love that the ingredients are lower in fat so its indulgent yet better for you than a calorie laden dessert. I have celiac so I love that the recipe is GF and not with complicated ingredients (like most GF recipes are).
The Clean Eating Couple says
Thank you so much! We wanted this recipe to be super simple and still be delicious so I’m glad you enjoyed it!
Liz says
This looks amazing! Will definitely make for a holiday dessert, and might try for myself even, wondering if this will be OK with dairy free cream cheese… I’ll update if I try it that way!!
The Clean Eating Couple says
I haven’t tried it but I think it might work! If you try it let me know 🙂
Shaun says
This is seriously SO yummy! Honestly, I enjoy it more than real cheesecake! So super simple too
The Clean Eating Couple says
Thanks, Shaun! Glad you liked it!
Erica B says
Made these for the first time last night and they are so delicious!!! Super quick & easy to make too!
The Clean Eating Couple says
So happy you liked them, Erica!
Berni says
Can I leave multiple reviews?! I hope so, as I made these again and brought them to the family party over the weekend and they were a huge hit. I somehow had more than enough mixture to fill all 12 this time around, so I did. More cheesecake anyone? 🙂 I just put the blueberries and raspberries on for garnishment as you show in your photo and they were so cute.
The Clean Eating Couple says
Thank you so much, Berni! I appreciate it!
Danielle says
These were great! I just did an oreo crust instead, but the cheesecake filling was a perfect consistency!
The Clean Eating Couple says
Wow that sounds yummy!!
Kim says
If you were to use this recipe for a full size cheesecake, would it work? If you’ve tried it, how long did you bake it? Thanks!
The Clean Eating Couple says
I’m not sure how that would work because I haven’t tried it! I think the crust would bake for a similar amount of time, but you might need to double the crust recipe to fit in a pan. You don’t bake the filling of this. Sorry I can’t be of more help!