Keto Pizza Casserole
Published October 17, 2021 • Updated February 28, 2026
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This keto pizza casserole skips cauliflower and ground beef entirely. Layers of cream cheese, marinara, pepperoni, and buttery pull-apart almond flour rolls on top that my kids actually request on Friday nights.
I got tired of every low carb pizza recipe starting with cauliflower or ground beef. Nothing wrong with either, but I wanted something that actually felt like pizza night, not a healthy compromise pretending to be one. So I built this around what makes pizza craveable: a thick cream cheese base, proper marinara, layers of melted mozzarella, and pepperoni that crisps at the edges.
The cream cheese layer is what sets this apart. I mix it with parmesan, Italian seasoning, and red pepper flakes until it’s smooth and creamy, then spread it across the bottom of the dish. It creates this rich, savory base that soaks up the marinara from above without getting watery. Think of it as the ‘crust’ replacement, except it adds flavor instead of just structure. If you like that layered, cheesy approach, my keto baked ziti uses a similar technique.
Then there are the pull-apart rolls on top. These are not fathead dough. The base is almond flour, but the reason they stay fluffy inside and get genuinely golden and crispy on top is the unflavored protein powder. It gives the dough structure that almond flour alone can’t. I roll them into small balls, pack them close together on top of the pepperoni layer, and brush everything with garlic butter before baking. They soak up juices from the marinara and cheese underneath, which gives you that pizza-dough bite in every piece.
I’ve made this for years and it works just as well for a Tuesday dinner as it does when I’m feeding extra people. The whole thing comes together in one casserole dish, and the leftovers reheat better than most keto dinners I make. If you’re looking for more casserole-style meals, my keto taco casserole and keto zucchini lasagna are both in the regular rotation at my house.
What I keep hearing from readers is that this doesn’t taste like a keto workaround. One reader, Steve, put it better than I could: ‘The whole casserole felt like actual pizza, not a keto compromise, which is not something I say lightly after four years of this.’ That’s the goal. Not a diet recipe that happens to be edible, but an actual dinner you’d make even if you weren’t counting carbs. If you love pizza nights, my keto deep dish pizza has a proper thick crust for when you want that extra base layer.
How to Make It
I measure out all my dry ingredients before I start mixing. The key to the pull-apart rolls is working quickly once you melt the mozzarella. If it starts to harden, microwave it for 10-15 seconds to soften it back up. I’ve re-microwaved it partway through mixing and it turns out fine. Roll the dough balls to about 1/2 to 3/4 inch and make sure they’re touching or nearly touching on top of the pepperoni layer. If your rolls come out soft inside, they were probably too big or too thick. Try making them smaller and lowering the oven by 25 degrees while adding a few extra minutes to the bake time.
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Keto Pizza Casserole Ingredients
4 cups shredded mozzarella cheese, divided -
16 oz cream cheese, softened
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1/2 cup grated parmesan cheese
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1 tablespoon Italian Seasoning
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1 teaspoon red pepper flakes
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3/4 cup low-carb marinara sauce
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3 oz pepperoni slices
Pull-Apart Keto Rolls Ingredients
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2 cups almond flour
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1/2 cup unflavored low-carb protein powder
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2 1/2 teaspoons baking powder
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2 teaspoons xanthan gum
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1 teaspoon salt
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1 egg
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1/2 cup shredded mozzarella cheese, melted
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1/2 cup unsalted butter, melted
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2 tablespoons sour cream
Butter Garlic Parsley Sauce Ingredients
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2 tablespoons butter, melted
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3 cloves garlic, minced
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2 tablespoons chopped parsley
Step by Step Instructions
Step by Step Instructions
Preheat oven
Preheat oven to 350 degrees. Spray a 8×10 casserole dish with cooking spray and set aside.
Cheese mixture
To a large bowl, mix together 2 cups shredded mozzarella cheese, cream cheese, grated parmesan cheese, Italian seasoning and red pepper flakes using an electric mixer until creamy and smooth.
Cheese layer
Spread cheese mixture evenly into the casserole dish.
Pizza sauce
Pour pizza sauce on top of the cheese layer and spread using the back of a spoon.
More cheese
Sprinkle 2 cups shredded mozzarella cheese on top of sauce in a even layer.
Pizza topping
Evenly lay down sliced pepperoni on to of the shredded cheese layer. Set aside.
Make pull-apart rolls
In a food processor, pulse together almond flour, protein powder, baking powder, xanthan gum and salt until combined. Add egg, melted cheese, butter and sour cream. Pulse until dough ball forms. NOTE: You can also mix the dough using an electric mixer. It will take longer to evenly combine.
Roll into balls
Pinch off dough and roll between the palms of your hands into 1/2 – 3/4 inch balls. Layer on top of the pepperoni, making sure the balls are touching or close to touching each other.
Buttery Garlic Sauce
In a small bowl, mix together melted butter, minced garlic and chopped parsley. Brush on top of the keto dough.
Bake
Bake in a 350 degree oven for 15-20 minutes or until the pull-apart rolls are golden brown.
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 freeze keto pizza casserole?
I freeze this regularly. Let it cool completely, then wrap tightly in foil and store in a freezer bag. When I reheat from frozen, I bake it covered at 350 degrees for about 40-50 minutes, then uncover for the last 10 to crisp the rolls back up. The rolls hold up better than I expected, though they won't be quite as crispy as fresh.
Can I make this ahead of time?
I've assembled this a full day ahead and kept it covered in the fridge. When you're ready, just add about 10 extra minutes to the bake time since it's going in cold. The cream cheese base actually sets up better when it's had time to chill, so the layers stay more distinct.
Can I make this in an air fryer?
I've done it in my air fryer at 350 degrees for about 8-12 minutes. Use a smaller baking dish that fits your basket and keep an eye on the rolls since they brown fast with the circulating air. I pull it when the rolls are golden and the cheese is bubbling underneath.
How do I keep the dough balls from being soft inside?
This is the most common question I get on this recipe. Usually it means the balls were too big or too thick. I roll mine to about 1/2 to 3/4 inch. If they're still soft, try lowering your oven by 25 degrees and baking a few minutes longer. That lets the inside cook through without burning the tops.
How do I keep melted mozzarella from hardening before I can mix it in?
I have all my dry ingredients measured and ready before I melt the cheese. That way I can add it immediately. If it starts to firm up, microwave it for another 10-15 seconds to soften it back up. I've re-microwaved partway through mixing and it still comes together fine.
Can I use a different type of cheese instead of mozzarella?
I've tested provolone and an Italian cheese blend in place of the mozzarella, and both work. Provolone gives you a slightly sharper flavor that I actually prefer sometimes. The texture changes a bit but it still melts and layers the same way.
What can I use instead of cream cheese?
I've swapped in mascarpone as a 1:1 replacement and it works well. The flavor is a touch milder. I've also tried ricotta, which works but makes the base layer a bit grainier. If texture matters to you, stick with cream cheese or mascarpone.
How do I store leftovers?
I keep mine in an airtight container in the fridge for up to 4 days. For reheating, I always go with the oven at 350 degrees over the microwave. The oven crisps the rolls back up. Microwave works if you're in a rush, but the rolls go soft.
Every keto pizza casserole I'd made before had a cauliflower base or ground beef. They were fine, just never something I wanted again. This one skips both and puts almond flour pull-apart rolls on top, which honestly sounded like a lot. Made it on a Friday night because I had everything and my kids had been begging for pizza all week. The rolls are what got me. Watching them puff up over the cream cheese and marinara layer, I had no idea how it was going to work. And then it did. I've made plenty of keto pizza casseroles and this is the first one where I finished my plate already thinking about when I'd make it again.
I started keto back in January and honestly the thing I kept grieving was pizza (not bread, not pasta, pizza specifically). Made this last week and I had a moment after the first bite where I just stopped. The cream cheese layer underneath the marinara is doing something I can't fully explain but it's rich in a way that hit me like a real slice would. I'm pretty new to cooking so I was nervous about the almond flour rolls on top but they puffed up golden and didn't fall apart when I scooped them out, which felt like a win. Four stars only because mine came out a little saltier than I expected, probably the parmesan I used, but I'd make this again without hesitation. I didn't think I'd find something that scratched that Friday night pizza itch this early into keto.
I've only got a 9x13 pan and I'm throwing this together for dinner tonight. Does the bigger dish affect the bake time on those pull-apart rolls on top, or will they still come out right?
If your oven runs hot, tent the foil at 20 minutes. Rolls brown faster than the casserole finishes, so covering for the last bit keeps things from getting overdone.
The flavor layers are spot-on, but my rolls sank into the filling during baking and lost that pull-apart texture I was expecting. Might try adding them in the last 15 minutes next time to keep them distinct. Otherwise solid.
The 15-minute drop-in works. I've done that when my filling runs a little loose. Smaller balls help too, mine are about 3/4 inch, anything bigger and they just get swallowed.
Stirred roasted garlic into the cream cheese layer on a whim and it completely changed the bottom half of this casserole. You get this savory, almost caramelized depth underneath the marinara that made me stop mid-bite and go right back in. I also added a layer of mushrooms between the sauce and the top mozzarella because I had them sitting there, and they just melted into everything in a way that was SO good. The almond flour rolls still puffed and crisped up even with the extra moisture from the mushrooms, which I did not expect to work out at all. I've made this three times now and keep tweaking something each time, but the roasted garlic in the cream cheese is staying permanently. Already thinking about a white pizza version with spinach and artichokes for next weekend.
My wife can't do dairy, so we'd need to swap the cream cheese and mozzarella. I've used dairy-free cream cheese before but never when it's basically the whole base layer. Does it still set up okay when baked or does it stay loose?
Dairy-free cream cheese works fine, it sets up once baked. Mozzarella's trickier. I'd go with Violife or Miyoko's shreds, not the store brand stuff.
My son called the rolls on top 'the good bread' and asked if we could just have those for dinner sometime. (They're almond flour. Didn't mention that.)
Friday night pizza was basically a religion in my house growing up. Boxes from the corner place, everyone crowded around the kitchen island, nobody caring about the grease on the cardboard. When I went keto three years ago I figured that version of Friday nights was just gone. Made this last week and the smell when it came out of the oven stopped me cold, that combination of pepperoni and Italian seasoning hitting the air like a memory I forgot I had. The pull-apart rolls on top are the part that really got me. I ate way more than I should have and sat there with zero guilt. This is my new Friday night.
That smell combo is why I stopped doing the cauliflower base. Friday nights deserve the real thing.
Swapped the pepperoni for hot Italian sausage and the rolls absorbed so much rendered fat it came out closer to deep-dish than casserole. Not what I was going for, but I'm keeping it.
That's an upgrade, not an accident. Hot Italian sausage renders way more fat than pepperoni, so of course the rolls absorbed it. That's the version I'd make on purpose.
I kept scrolling past this because I couldn't picture how almond flour rolls would work on top of a casserole. Made it on a whim last week anyway and they baked up golden and pull-apart, not what I expected. The cream cheese layer threw me off too, but it all kind of works. I'd probably add a little more marinara next time, but I'm already planning round two.
More marinara next time, yeah. I go closer to a full cup when I want it saucy. The cream cheese base absorbs a lot.
Was skeptical about almond flour pull-apart rolls actually working as a topping, but they came out genuinely golden with real pull-apart texture that I've never gotten from a fathead crust. The whole casserole felt like actual pizza, not a keto compromise, which is not something I say lightly after four years of this. Four stars, and I'm already thinking about what toppings to load in next time.
The roll skeptics always come around. I'd go sausage next time. It renders into the cream cheese layer in a way pepperoni just doesn't.
Pizza was what I was most sad to give up when I went keto. Made this on a cold Sunday night and texted my sister mid-meal because I needed someone to know, I was not ready for it to be this good. The cream cheese base is SO rich it doesn't feel like you're missing anything.
Ha, the mid-meal text. The cream cheese does most of the work here. Add an extra pinch of red pepper flakes next time if you want a little heat under all that richness.
I've made this 4 times now and still don't bother with actual pizza crust anymore. Those almond flour rolls on top get so crispy.
The crispy tops are the best part. I brush them with garlic butter before baking sometimes.
just made this. it was good. but, i have a couple questions…1) i dont have a food processor so used my hand mixer…how do you keep the melted mozzarella soft long enough to incorporate? 2) my keto rolls were soft inside (maybe a little moist). did i do something wrong? any advice appreciated
I usually have all of my ingredients measured out and ready to combine before I mix everything. You could microwave the cheese right before you add it or I have even re-microwaved it before adding it. If the dough was still a little soft, they might have been too big or thick or you could try lowering the oven temperature a bit and cooking them longer.