Mini Keto Cheesecakes
Published March 14, 2025 • Updated March 15, 2026
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I make these keto cheesecake bites in a mini muffin tin, and they taste like real New York cheesecake in one perfect bite. The oat fiber crust actually holds up when you peel the liner, which is more than I can say for most low carb versions I've tried.
Cheesecake is one of my all-time favorite desserts. I have a classic keto cheesecake that I’ve been making for years, but the problem with a full-sized one is that it sits in my fridge all week and I keep going back for more. These mini cheesecakes fix that. I bake them in a mini muffin tin so each one is a single, portioned bite of creamy New York-style cheesecake that I can grab without cutting into a whole cake.
What makes it keto
- Graham cracker-style crust without the carbs. I spent months testing almond flour crusts, and they kept crumbling apart when I peeled the liner back. Adding oat fiber was the fix. It gives the crust real structure and a subtle graham cracker flavor that almond flour alone never achieves. If you don’t have oat fiber, coconut flour works as a substitute, though the flavor is slightly different.
- Creamy cheesecake filling at 1.4g net carbs per bite. The filling is exactly what you’d expect from a classic cheesecake: smooth, tangy, and ultra-creamy. I use Greek yogurt in mine for a slightly lighter texture, but sour cream works too. Sugar-free sweetener keeps the carbs down without sacrificing that rich cheesecake taste.
- Blackberry syrup that stays smooth. I top these with a quick stovetop syrup made from fresh blackberries and allulose. I specifically chose allulose because erythritol-based sweeteners crystallize when they cool and leave a gritty film. Allulose stays silky even after a night in the fridge.
Built for portion control
The mini size actually changes how people eat cheesecake. Nobody cuts a sliver and puts the rest back. They grab one, eat it, and they’re done. My family asks for these on Friday nights, and I keep a batch in the freezer so I can pull out a few without making a production of it. One reader, Brianna, told me the crust held up in a way she wasn’t expecting from almond flour, and she sent the recipe to her mom who taught her to make cheesecake in the first place. That’s the kind of feedback that tells me this one works.
If you love cheesecake desserts, I have a few other recipes worth trying. My keto chocolate trifle layers cheesecake filling with chocolate cake. The keto strawberry shortcake pairs a creamy base with fresh berries. My keto trifle is another layered option if you like building desserts. And for fall, my keto pumpkin cheesecake is the one I make every October.
Explore 685+ keto recipe videos with step-by-step instructions, tips, and tricks to make keto easy.
Keto Graham Cracker Crust Ingredients
1 1/2 cups almond flour -
3 tablespoons oat fiber, or coconut flour
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1/4 cup brown sugar substitute
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1/2 teaspoon xanthan gum
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1/4 teaspoon salt
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4 tablespoons unsalted butter, chilled & cubed
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1 teaspoon vanilla extract
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mini muffin pan
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mini muffin liners
Keto Cheesecake Filling Ingredients
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12 oz cream cheese, softened to room temperature
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2/3 cup sugar-free sweetener
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1/3 cup plain Greek yogurt
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1 large egg, room temperature
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1 large egg yolk, room temperature
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1 tablespoon fresh lemon juice
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1/2 teaspoon vanilla extract
Fruit Topping Ingredients
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6-8 oz fresh blackberries (about 1 cup)
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1/4 cup water
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1/3 cup powdered allulose sweetener
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2 teaspoons arrowroot powder
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squeeze lemon juice
Step by Step Instructions
Step by Step Instructions
Line a mini muffin tin
Preheat oven to 325°F. Line a 24-cup mini muffin tin with paper liners. Set aside.
Keto graham cracker crust
Add almond flour, oat fiber or coconut flour, brown sugar, xanthan gum and salt to a food processor. Give a few quick pulses to combine. Add butter and vanilla, pulse until combined. The crust is pulsed enough when the mixture will pack and stick together when you press it together with your fingers.
- 1 1/2 cups almond flour
- 3 tablespoons oat fiber or coconut flour
- 1/4 cup brown sugar substitute
- 1/2 teaspoon xanthan gum
- 1/4 teaspoon salt
- 4 tablespoons unsalted butter, chilled & cubed
- 1 teaspoon vanilla extract
Press the crust into the muffin pan
Add about ½-1 tablespoon of crust to each muffin cup. Press the crumbs firmly into each liner. This makes enough for 28, so you will have some left over.
Cheesecake filling: cream the cheese
For the cheesecake filling, add cream cheese and sugar-free sweetener to a medium/large bowl. Using an electric mixer, mix until combined and creamy, about 1-2 minutes.
- 12 oz cream cheese, softened to room temperature
- 2/3 cup sugar-free sweetener
Cheesecake filling: remaining ingredients
Add yogurt, egg, egg yolk, lemon juice and vanilla. Mix just until combined, don’t overmix.
- 1/3 cup plain Greek yogurt
- 1 large egg, room temperature
- 1 large egg yolk, room temperature
- 1 tablespoon fresh lemon juice
- 1/2 teaspoon vanilla extract
Bake mini cheesecakes
Divide the batter evenly on top of the cooled crusts. Fill each cavity to the top since they won’t overflow when baking. Bake at 325°F for 20-22 minutes until puffed and lightly set around the edges. Remove and let cool completely at room temperature. Once cooled, refrigerate until cooled and completely set.
Make the fruit topping
Combine blackberries, water, allulose sweetener, arrowroot powder and lemon juice in a small saucepan. Bring to a simmer over medium heat and cook, stirring occasionally until thickened and bubbly. Cool and refrigerate until ready to serve. Top each mini cheesecake with a dollop of fruit topping.
- 6-8 oz fresh blackberries (about 1 cup)
- 1/4 cup water
- 1/3 cup powdered allulose
- 2 teaspoons arrowroot powder
- squeeze lemon juice
Nutrition disclaimer
The nutrition information provided is an estimate and is for informational purposes only. I am a Doctor of Pharmacy (Pharm.D.); however, this content is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always consult your physician or other qualified health provider before making any lifestyle changes or beginning a new nutrition program.
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Get My Macros + Recipes →Frequently Asked Questions
Can I make these without a crust?
I've made them crustless plenty of times, and they're great that way. You save on carbs too. Just make the filling, pour it into the lined cups, and bake at the same temperature. The filling sets up on its own without any crust underneath.
Are these gluten free?
Yes. I use almond flour and oat fiber in the crust, and both are naturally gluten free. If you swap the oat fiber for coconut flour (which I've done), it stays gluten free. Nothing in the filling contains gluten either.
Why did my mini cheesecakes crack on top?
I've had this happen when I overfilled the cups. The filling puffs as it bakes, and if there's too much in there, the surface stretches and cracks. I fill each cup right to the top of the liner but not above it. I also bake at 325 degrees, which is lower than a lot of cheesecake recipes. That gentler heat helps them set without the surface splitting.
Can I use sour cream instead of Greek yogurt?
I've used both. Sour cream makes the filling a touch richer and denser, which I actually prefer some days. Greek yogurt gives it a slightly lighter feel. Either works, same amount, no other changes needed.
Can I make these in a regular-sized muffin tin?
I haven't baked these in a standard muffin tin yet, but the filling and crust work at any size. You'd need to increase the bake time (I'd start checking around 25-28 minutes) and use more crust per cup. The texture and flavor stay the same, just bigger portions.
Can I add other flavors like peanut butter or pumpkin?
I've swirled peanut butter into the filling before baking and it works really well. About a tablespoon of natural peanut butter mixed in before dividing into cups is enough. For pumpkin, I have a separate keto pumpkin cheesecake recipe with the spice ratios already dialed in. I've also made the topping with raspberries and strawberries using the same method. My keto strawberry cake uses a similar strawberry approach if you want more ideas.
Can I skip xanthan gum in the crust?
You can, but the crust will be more crumbly when you peel the liner. I've made batches without it and the flavor is the same. The crust just flakes instead of holding its shape. Guar gum works as a 1:1 substitute if you have that on hand.
How many carbs are in each bite without the syrup?
When I tracked it, each bite without the syrup comes out to just 1 gram of net carbs. With the crust, it's 1.4g. That's the number I use when I'm logging my macros for the day.
The oat fiber crust is what keeps bringing me back. I've made these probably six times now and it still holds when you peel the liner, which is more than I can say for most low carb versions I've tried. Batch seven coming this weekend.
Six batches and still going. The xanthan gum in that crust is what makes it peel clean. Took me a while to nail that ratio.
My mom made mini cheesecakes every Christmas, graham cracker crust, the whole thing. I'd basically banned myself from thinking about them after going keto. This oat fiber crust has that same buttery press-in texture and I was not prepared. Made my whole week.
Tough act to follow, your mom's Christmas cheesecakes. The press-in texture was the last thing I figured out on this one.
I have everything except xanthan gum. Is it essential for the crust, or can I skip it?
My grandmother's cheesecake was the birthday tradition in our family, full-size with a thick graham cracker bottom, and when I went keto I just kind of quietly accepted that was over. Made these last week and sat there with one of the little ones on my plate, just holding it for a second before I ate it. The crust held up and had this crunch I wasn't expecting (almond flour has let me down before). A few of mine cracked on top because I overfilled the cups, which is entirely on me. But the filling tasted close enough to what I remembered that I already sent the link to my mom, who taught me to make cheesecake in the first place, and she doesn't believe me yet. She'll make it and then she'll call me and she'll believe me.
Lost count of how many batches I've made at this point. The crust gets this little crunch after the six minutes in the oven and it's freaking addictive. One per night, every night, at 1.4g net carbs, I have zero reason to stop.
1.4g net carbs is doing a lot of... wait, no. That crust crunch is the oat fiber. Almond flour alone never gets there.
Room temp cream cheese is non-negotiable. Cut it into cubes, let it sit 15 minutes. My second batch came out way silkier.
Silkier is the right word. I leave the cubes out while the oven preheats and it does the same thing. Cold cream cheese is what makes the filling go grainy.
Made probably four or five keto cheesecake recipes over the past couple years and the crust is always the weak point. Either it crumbles when you peel the liner, or it compresses into something dense and flavorless. The oat fiber here actually gives it some body and it bakes up with a little crunch. Filling unmolded cleanly, texture was right. I'm done looking.
The oat fiber was the fix I didn't expect either. Almond flour alone just collapses when you peel the liner.
Are these gluten free if I use the coconut flour.
Yes!