Here’s a complete high-protein Deep-Dish Pizza Cupcakes recipe that’s indulgent, savory, and packed with protein. These are perfect as a snack, meal prep, or a fun party treat.
High-Protein Deep-Dish Pizza Cupcakes
Ingredients
For the “Crust”:
- 1 cup almond flour (or whole wheat flour if you prefer)
- 1/4 cup unflavored or savory protein powder (whey or plant-based)
- 1 tsp baking powder
- 1/2 tsp garlic powder
- 1/2 tsp onion powder
- 1/4 tsp salt
- 1 large egg
- 2 tbsp olive oil
- 2–3 tbsp unsweetened almond milk (adjust for consistency)
For the Filling:
- 1/2 cup low-sodium marinara sauce
- 1 cup shredded part-skim mozzarella cheese
- 1/2 cup cooked lean protein (diced chicken breast, turkey pepperoni, or lean sausage)
- 1/4 cup diced bell peppers (optional)
- 1/4 cup sliced mushrooms (optional)
- 1 tsp Italian seasoning
For Topping:
- 1/4 cup extra mozzarella cheese
- Fresh basil or parsley (optional, for garnish)
Instructions
- Preheat Oven
- Preheat your oven to 375°F (190°C).
- Grease a 12-cup muffin tin with cooking spray or line with silicone muffin liners.
- Prepare the Crust
- In a medium bowl, whisk together almond flour, protein powder, baking powder, garlic powder, onion powder, and salt.
- Add the egg, olive oil, and almond milk. Mix until it forms a thick, slightly sticky dough. Add a little more milk if too dry.
- Assemble Base in Muffin Cups
- Divide dough evenly among muffin cups.
- Press dough into the bottom and up the sides, forming a cup shape for your “pizza crust.”
- Add Filling
- Spoon 1–2 tbsp marinara sauce into each crust.
- Top with diced chicken or turkey pepperoni, bell peppers, mushrooms, and 1 tbsp mozzarella cheese.
- Sprinkle Italian seasoning on top for flavor.
- Bake
- Bake in the preheated oven for 15–18 minutes until the crust is lightly golden and cooked through.
- Add Topping
- Remove from oven, sprinkle additional mozzarella cheese on top, and bake another 3–5 minutes until cheese melts and is slightly bubbly.
- Cool and Serve
- Let cupcakes cool for 5 minutes in the pan before removing.
- Garnish with fresh basil or parsley if desired.
Nutrition Estimate (per cupcake, 12 servings)
- Calories: ~180 kcal
- Protein: ~15g
- Fat: ~10g
- Carbs: ~7g (mostly from almond flour and vegetables)
Pro Tips
- Use high-protein cheese or add extra egg whites in the crust for more protein.
- Swap marinara sauce for low-sugar, high-protein tomato sauce to reduce carbs.
- Perfect for meal prep—store in fridge up to 4 days or freeze for longer.

