Cottage Cheese Flatbread Pizza – {High-Protein & Gluten-Free!}

As much as I love my Two Ingredient Pizza Dough when I’m craving pizza, sometimes I want something quicker, lower in carbs, and higher in protein! That’s why I love this cottage cheese flatbread pizza recipe. You blend cottage cheese and eggs into a batter, bake it into a flatbread-style crust, then add sauce, cheese, and pepperoni and melt everything together.

The crust comes out sturdy with golden edges, and it’s surprisingly filling. It’s also very forgiving, which is nice when you’re hungry and not in the mood to make dough!

Before You Get Started

A few quick setup notes so the crust bakes up sturdy and not watery.

• Pan choice: Use a 9×13 baking sheet lined with parchment paper, and fold the parchment up at the edges so the batter stays contained.
• Cottage cheese texture: If your cottage cheese looks extra watery, drain it briefly so the crust sets up better. Watery cottage cheese can lead to a softer bake!
• Blend until smooth: You want the mixture fully blended so it bakes evenly and doesn’t feel lumpy.
• Topping prep: Have your sauce, cheese, and pepperoni ready before the crust comes out of the oven. The second bake is quick!

How to Make Cottage Cheese Flatbread Pizza

This is a two-bake situation: crust first, toppings second.

1. Preheat And Prep The Pan

Preheat the oven to 350°F. Line a 9×13 baking sheet with parchment, folding up the edges.

Pro tip: A light spritz of cooking spray on the parchment helps with easy release.

2. Blend The Flatbread Batter

Add cottage cheese, eggs, Parmesan (if using), garlic powder, Italian seasoning, salt, and pepper to a blender or food processor. Blend until smooth.

Pro tip: Scrape down the sides once so the seasonings fully mix in.

3. Bake The Crust

Pour the mixture onto the lined baking sheet and spread into an even layer. Bake 30–35 minutes, until the edges are golden and the center looks set.

Pro tip: The center should look dry and set, not glossy or wet.

4. Cool Briefly, Then Top

Let the crust cool 2–3 minutes so it settles a bit. Spread on marinara, sprinkle mozzarella, and add turkey pepperoni.

Pro tip: If the crust is very puffy, that short cool-down helps it relax before topping.

5. Melt The Cheese

Return to the oven for 5–7 minutes, until the cheese is melted. Rest for a couple of minutes, then finish with fresh basil.

Pro tip: Letting it rest makes it easier to slice cleanly.

Air Fryer Method

If you’ve got an air fryer with a tray/basket big enough for a smaller portion, this works great.

Bake the crust in a parchment-lined air fryer-safe pan at 350°F, checking early since air fryers run hot. Add toppings and cook just until the cheese melts. (I usually treat this as a “make a smaller pizza” method, not a full 9×13 batch.)

Recipe Tips and Tricks

Helpful tweaks, upgrades, and “make it yours” ideas.

• Sauce swap: Use Twenty Minute Homemade Marinara Sauce if you want a brighter, more homemade sauce vibe.
• Spice it up: Add black pepper or red pepper flakes to the batter, or sprinkle flakes on top after baking.
• Go veggie-heavy: Add quick-cook toppings like chopped spinach (squeezed dry), Easy Sautéed Mushrooms with Garlic Butter, or bell peppers (thinly sliced) so you don’t add moisture that makes the pizza soggy.
• Change the protein: Turkey pepperoni is classic, but chopped cooked chicken sausage or deli turkey also works.
• Crispier top: Broil for 1–2 minutes at the end if you want browned cheese bubbles. Watch it closely.
• Add extra protein: Top the pizza with sliced Easy Grilled Chicken Breasts or Slow Cooker Italian Shredded Beef for an easy protein boost!
• BBQ chicken twist: Swap marinara for BBQ sauce, use mozzarella (or a little cheddar), and top with chopped Crispy BBQ Baked Chicken Thighs for a fun BBQ chicken pizza vibe!

Serving Ideas

A few easy sides that make this feel like a full dinner.

Storage & Reheating

Here’s how to keep the slices tasty.

• Storage: Store slices in an airtight container in the fridge for up to 3 days.
• Freezer: Freeze slices on a sheet pan, then transfer to a freezer bag for up to 2 months.
• Reheating: Reheat in the oven or air fryer until hot and the edges crisp back up. The microwave works, but the crust stays softer.