Healthy Margherita Pizza Recipe with Whole-Wheat Crust

This healthy Margherita pizza recipe makes two crisp, whole-wheat pies topped with tomato, mozzarella, and fresh basil. It keeps the familiar Italian-style combination simple, while a homemade crust and a measured amount of cheese let each ingredient shine.

Ingredients

1½ cups (180 g) whole-wheat flour
1 cup (120 g) bread flour, plus a little extra for shaping
¾ cup (180 ml) warm water, about 105–110°F (41–43°C)
1 teaspoon (3 g) instant or active dry yeast
1 teaspoon (7 g) honey or sugar
2 teaspoons (10 ml) olive oil, plus 1 teaspoon (5 ml) for brushing
¾ teaspoon (4.5 g) fine salt
¾ cup (180 g) canned crushed tomatoes, preferably drained briefly if very watery
6 ounces (170 g) fresh mozzarella, well drained and torn or sliced thin
2 tablespoons (10 g) finely grated Parmesan, optional
½ cup (10 g) loosely packed fresh basil leaves
1 teaspoon (5 ml) olive oil, for finishing, optional
1 teaspoon (3 g) cornmeal or flour, for dusting the baking surface, optional

Instructions

Mix the dough. In a large bowl, stir together the warm water, yeast, and honey. If using active dry yeast, leave it for 5 minutes until it looks lightly foamy; instant yeast can be mixed in and used right away. Add both flours, 2 teaspoons olive oil, and the salt. Stir until a rough dough forms and no dry pockets of flour remain. The dough should feel soft and slightly tacky, not wet and gluey. If it is unusually sticky, add bread flour a teaspoon at a time rather than adding a large amount at once.
Knead and let it rise. Turn the dough onto a lightly floured counter and knead for 8–10 minutes, pushing it away with the heel of your hand and folding it back over itself. It is ready when smoother and elastic; a small roughness from the whole-wheat flour is normal. Lightly oil the bowl, return the dough, and cover it. Let it rise at room temperature for 60 minutes, or until puffy and close to doubled. Whole-wheat dough may not look as airy as dough made entirely with white flour, so judge by its visible expansion rather than expecting a precise size.
Heat the oven and prepare the toppings. During the rise, place a pizza stone or steel on a rack in the upper-middle part of the oven and heat to 500°F (260°C) for at least 30 minutes. If you do not have a stone or steel, use a heavy baking sheet turned upside down and preheat it too. Drain the mozzarella and pat it dry with paper towels; excess moisture can make the center soggy. Stir the crushed tomatoes briefly to loosen them. Keep the basil aside for after baking so its leaves stay fragrant and green.
Divide and shape the crusts. Once the dough has risen, turn it onto a lightly floured counter and divide it into two equal pieces. Shape each into a ball, then press and stretch one ball into a roughly 10-inch (25 cm) round. Work from the center outward, leaving a slightly thicker rim. If the dough keeps shrinking, cover it and let it relax for 5 minutes before continuing. Repeat with the second piece. Avoid using a rolling pin if you want a more open, uneven edge, but it is fine to roll the dough if that is easier for you.
Top the pizzas. Carefully transfer one dough round to a piece of baking parchment or a pizza peel dusted with cornmeal or flour. Spread about ⅜ cup (90 g) crushed tomatoes in a thin layer, leaving the rim bare. Use roughly half the mozzarella and Parmesan, if using. Keep toppings modest and spread them evenly; a thick blanket of cheese or a pool of tomato sauce can weigh down the crust. Assemble the second pizza the same way just before it goes into the oven.
Bake, finish, and serve. Slide the first pizza onto the hot stone, steel, or inverted baking sheet. Bake for 9–11 minutes, until the crust is browned at the edges and the cheese is melted with a few golden spots. Baking times vary with ovens and surfaces, so check the underside as well as the top. Repeat with the second pizza. Scatter basil over the hot pizzas and, if desired, finish with the remaining teaspoon of olive oil. Let each pie sit for 2 minutes so the cheese settles, then slice and serve while warm. The brief settling time can happen while the second pizza finishes baking.

Tips

Drain fresh mozzarella thoroughly. Fresh mozzarella gives the pizza its tender, milky topping, but it contains more moisture than low-moisture cheese. Drain it in a sieve while the dough rises, then pat it dry. If you need a reliably crisp center, substitute 6 ounces (170 g) part-skim low-moisture mozzarella; it melts more evenly and tastes less delicate.
Use a light hand with the sauce. The recipe uses less than a half cup per pie because an overly thick layer can make whole-wheat dough damp in the middle. If your crushed tomatoes are especially loose, drain them in a fine sieve for 5–10 minutes. Do not cook the sauce first; its fresh tomato flavor works well here.
Make shaping easier. Whole-wheat flour absorbs water gradually, and dough can feel firmer after a rest. If it resists stretching, give it a covered 5-minute pause rather than pulling hard and tearing it. A little flour on the counter helps, but too much can leave dry flour on the finished crust.
Keep the oven hot. A fully heated stone or steel helps the base brown before the toppings release too much moisture. Use oven mitts when loading the pizza, and do not touch the hot surface. If your oven does not reach 500°F (260°C), set it to its highest available temperature and expect a few extra minutes of baking.

Serving Suggestions

Serve the pizza hot, cut into wedges, with a green salad dressed with lemon juice and olive oil or a simple bowl of sliced cucumbers and tomatoes. The fresh, crisp side balances the soft cheese and chewy crust without competing with the basil. For a fuller meal, add roasted vegetables such as zucchini, peppers, or broccoli. Put extra Parmesan, black pepper, and chili flakes on the table so everyone can season a slice to taste. If serving both pizzas at once, bake them in sequence and keep the first on a wire rack in a warm oven; a rack helps prevent steam from softening its bottom.

Variations

Use all whole-wheat flour: Replace the bread flour with 1 cup (120 g) additional whole-wheat flour. The crust will be denser and more earthy, and the dough may need 1–2 teaspoons (5–10 ml) extra water if it feels dry while kneading. Add water gradually; a soft, workable dough is better than a stiff one.

Try a different tomato base: Crushed tomatoes keep the topping quick and bright. For a smoother finish, use ¾ cup (180 g) passata or strained tomatoes. If using thick tomato paste, thin 2 tablespoons (30 g) with 2 tablespoons (30 ml) water; paste alone is too concentrated and can taste harsh.

Change the cheese: Use part-skim low-moisture mozzarella for a less milky, more evenly melted topping, or replace up to half the mozzarella with thinly sliced provolone. Provolone tastes sharper, so keep the tomato and basil portions unchanged and avoid adding too much salty Parmesan.

Add vegetables carefully: Thin slices of mushroom, bell pepper, or zucchini can go on the pizza, but keep the total additions to about ½ cup (50–75 g) per pie. Cook watery vegetables first and blot them dry. Too many raw toppings release moisture and can leave the center underbaked.

Storage and Reheating

Let leftover slices cool briefly, then refrigerate them in a covered container within 2 hours of baking. Store for 3–4 days. For the best texture, place parchment between stacked slices; avoid leaving the pizza at room temperature for extended serving. You can freeze slices in a single layer until firm, then wrap or transfer them to a freezer-safe container for up to 2 months for best quality. Thaw frozen slices overnight in the refrigerator or reheat them directly from frozen.

For a crisp base, warm refrigerated slices in a skillet over medium-low heat for 3–5 minutes, covering the pan briefly to melt the cheese. Alternatively, bake on a sheet at 375°F (190°C) until hot. Reheat leftovers to 165°F (74°C), the USDA FSIS recommended temperature, checking the center of a slice with a food thermometer. A microwave is convenient, but it softens the crust; use short bursts and expect a less crisp result.

Frequently Asked Questions

Can I make the dough ahead?

Yes. After kneading, cover the dough and refrigerate it for up to 24 hours rather than giving it the room-temperature rise. Let it sit at room temperature for about 30–45 minutes before shaping so it is easier to stretch. Chilled dough may rise slowly, so look for a puffy appearance instead of relying only on the clock.

Can I use fresh tomatoes instead of canned crushed tomatoes?

Yes, but choose ripe tomatoes that are not overly watery. Grate them on the large holes of a box grater or chop them finely, then drain excess juice for several minutes. Use about ¾ cup (180 g) prepared tomato per pizza as written. A watery fresh tomato topping can make the middle of the crust soft.

Why is the center of my pizza soggy?

The most common causes are wet mozzarella, too much sauce, a cool baking surface, or an overloaded pizza. Drain and dry the cheese, spread a thin tomato layer, preheat the stone or baking sheet thoroughly, and leave space between toppings. If the rim is done but the middle still looks pale, bake the pizza for another minute or two and check the bottom.

Can I make this without a pizza stone?

Yes. Preheat a heavy, rimless baking sheet upside down so the pizza can slide onto its hot flat surface. A regular baking sheet also works, though it may take longer to brown the base. Parchment makes loading easier; check its package directions for high-temperature use and trim any excess paper that could reach an oven element.

Is this the same as “margarita” pizza?

The classic name is Margherita, and the pizza is recognized by its tomato, mozzarella, and basil topping. “Margarita pizza” is a common search spelling, but it refers to the same familiar style in this recipe. Regional and home versions vary in crust, cheese, and tomato preparation, so the proportions here are a practical home-oven approach rather than a claim that there is only one correct version.

More recipes to cook

Safety notes: safe minimum internal temperatures from USDA FSIS; raw and undercooked fish guidance from the U.S. FDA. Food safety notes

Spotted an error? Tell us and we will correct it (corrections policy).