This keto pepperoni pizza with fathead crust is one of my go-to dinners when I want real pizza comfort without a traditional wheat crust. The crust is mozzarella-based, made with coconut flour and psyllium husk, and unlike many fathead dough recipes, this version doesn’t use cream cheese.

On top, it’s kept simple: tomato sauce, more mozzarella, pepperoni, and sliced red onion. Nothing complicated, nothing you need a special trip to the store for. It’s the kind of pizza I make when I want something that actually feels like pizza, not a sad low carb substitute.

Watch Me Make This Keto Pepperoni Pizza

If you’d rather see the whole process than read it, I filmed myself making this one from start to finish.

Why I Like This Low Carb Pizza

• Mozzarella-based crust that’s genuinely cheesy, not just “crust that happens to have cheese in it”
• Low carb, made with coconut flour instead of traditional wheat flour
• No cream cheese, so it’s a simpler, more straightforward dough
• Short ingredient list, nothing hard to find
• Toppings are easy to customize once you’ve got the base down
• Quick bake time, with 10 to 15 minutes in the oven

Here’s everything that goes into the crust and the toppings. Quantities below are exactly what I use.

For the Fathead Crust

• 2 cups shredded mozzarella cheese
• 2 tbsp coconut flour
• 1/2 tbsp psyllium husk
• 1 egg

A few notes that actually matter here: use a mozzarella that melts easily, since the whole dough depends on it going smooth and pliable. Coconut flour behaves nothing like almond flour, it’s far more absorbent, so if you’re tempted to swap it, don’t treat it as a 1:1 substitution. And the psyllium husk isn’t optional filler, it’s what gives the dough enough structure to roll out and hold together.

For the Toppings

• 1/2 cup tomato sauce
• 5 slices pepperoni
• 1/2 red onion, sliced
• 1/2 cup shredded mozzarella cheese

If you track carbohydrates, check the label, as carb counts can vary between tomato sauces.

Instructions

1. Preheat your oven to 392°F (200°C). Line a baking sheet with parchment paper.

2. Melt the mozzarella:
    • Microwave method: Heat for 2 minutes, stirring halfway.
    • Stovetop method: Melt over low heat, stirring until smooth.

3. In a bowl, mix the melted mozzarella with coconut flour, psyllium husk and egg until a dough forms.

4. Grease your hands with olive oil and shape the dough into a ball.

5. Roll the dough between two sheets of parchment paper to your desired thickness.

6. Spread the tomato sauce over the dough.

7. Add shredded cheese, pepperoni, and tomato slices.

8. Bake for 10–15 minutes, until the crust is golden and the cheese is melted and bubbly.

Tip: For a crispier crust, bake for an extra 2–3 minutes!

1. Melt the Mozzarella

Preheat your oven to 392°F (200°C) and line a baking sheet with parchment paper.

Melt the mozzarella in the microwave for about 2 minutes, stirring halfway through. You can also melt it on the stovetop over low heat, stirring until smooth.

2. Make the Fathead Dough

Add the coconut flour, psyllium husk, and egg to the melted mozzarella. Mix until everything comes together into a dough.

Work with the mixture while the mozzarella is still warm, as it becomes harder to shape once it cools.

3. Roll Out the Crust

Lightly oil your hands if the dough feels sticky and shape it into a ball.

Place the dough between two sheets of parchment paper and roll it out to your preferred thickness.

4. Add the Toppings

Remove the top sheet of parchment paper.

Spread the tomato sauce over the crust, then add the shredded mozzarella, pepperoni, and sliced red onion.

5. Bake the Pizza

Bake for 10 to 15 minutes, until the crust is golden and the mozzarella on top is melted and bubbling.

If you prefer a crispier crust, leave it in the oven for another 2 to 3 minutes, keeping an eye on it.

My Tips for a Better Fathead Pizza Crust

• Work with the dough while the mozzarella is still warm, it gets stiff and harder to shape once it cools
• Roll it between parchment paper rather than on a floured surface, it saves you the mess
• If the dough sticks to your hands, a little oil solves that fast
• Don’t overload the pizza with very wet toppings, they can make the crust soggy in the middle
• A couple of extra minutes in the oven gives you a noticeably crisper base if that’s what you’re after

Easy Topping Variations

The pizza in the photos is exactly what’s listed above, but if you want to switch it up another time, these all work well on a fathead crust:

• Mushrooms
• Olives
• Bell peppers
• Cooked chicken
• Ham
• Fresh basil
• Extra mozzarella

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Helpful Tools for Making This Pizza

Baking Sheet: Used to bake the pizza once it’s topped, a sturdy, even-heating sheet pan helps the crust cook through evenly.
A baking sheet like this one

Rolling Pin: If you use one to roll out the dough between the parchment sheets, a rolling pin like this one

How to Store and Reheat Leftover Keto Pizza

Leftover slices keep well in the refrigerator for a few days in an airtight container. For reheating, the oven or an air fryer will get you the closest to that fresh-baked texture, since the crust can go a bit soft in the microwave. The microwave is still the fastest option if you’re short on time, just don’t expect the same crispness.

More Low Carb Recipes to Try

If you enjoy recipes like this one, here are a few more from BySuzike Bites:

• Keto Fried Cabbage
• Keto Eggplant Lasagna
• Easy Low Carb Cocoa Coconut Truffles
• Strawberry Peanut Butter Chocolate Bonbons
• 2 Easy Meal Prep Jar Salads

Frequently Asked Questions

Is fathead pizza keto?
This recipe is designed as a low carb, keto-style pizza using mozzarella, coconut flour, psyllium husk, and egg instead of a traditional wheat crust. Exact carb counts will depend on the tomato sauce, pepperoni, mozzarella, and serving size you use.

Ready to Make It?

That’s the whole recipe, real ingredients, no traditional wheat crust, and a base that actually holds together. If you make it, let me know how it turns out. And if you’re working on keeping your carbs down across the board, not just at pizza night, the Low Carb Food Comparison Pack is there to make those everyday choices a little easier. For more low carb ideas like this one, check out the rest of BySuzike Bites.