Whole fresh basil leaves go on a pizza after baking, and the leaves that have to be on it before baking get tucked under the cheese where the oven cannot reach them directly. Put basil on top of the cheese and send it into a hot oven and you get black, brittle confetti with almost no smell left in it. The choice of before or after baking comes down to where the aroma ends up.
That aroma is the whole reason basil is on the pizza, so it is worth protecting.
The aroma that leaves in the oven
Basil's smell lives in a volatile oil held in glands on the surface of the leaf. Crush a leaf between your fingers and you release some of it into the air. Put the leaf on a surface hot enough to brown cheese and you release all of it, in seconds, into your kitchen instead of into the pizza.
The oil and the plant fibre respond to heat on different timescales. At oven temperatures, around 250 °C (480 °F) or higher, the volatile compounds evaporate within moments while the cellulose stays behind. What is left is the leaf's structure with almost nothing aromatic in it. Heat separates what you can smell from what you can see, and what is left on a scorched leaf is the plant material without much of what made it worth using.
Colour goes at the same time. The leaf blackens where the cell walls rupture and the chlorophyll degrades, which is why oven-exposed basil looks burnt long before the pizza is done.
Leaves under the cheese
Basil can go on before the bake as long as it never sees direct radiant heat. Lay whole leaves on the sauce and cover them with mozzarella, and they steam instead of roasting. They come out olive green and soft, with a mellower, cooked flavour that runs through the cheese instead of sitting on top of it.
Two habits make this work. Use whole leaves, never chopped, because cut edges oxidise and blacken faster. Brush or toss them in a little olive oil first, which slows moisture loss and keeps the surface from drying out.
This is the version to use when you want basil in every bite, woven through the cheese. It is also the only sensible option on a pizza that is going to be reheated, since a raw leaf added after the first bake will burn during the second.
Leaves after the bake
The stronger version, for almost every pizza, is basil added the moment the pie comes out. The residual heat from the cheese is enough to wake the oil up without cooking it off, so you get the smell as the pizza reaches the table.
Tear the leaves by hand instead of cutting them with a knife. Torn edges bruise less cleanly than a blade's crush and hold their green longer, and torn pieces sit better on an uneven surface. Scatter them across the whole pie. A pile in the middle leaves most slices bare. Do it after slicing, not before, or the wheel will drag half of them off.
Small leaves go on whole. Large ones can be torn in half, though a whole leaf holds its aroma longer than two pieces of the same leaf.
Pesto, basil oil and the dried version
Basil that has already been turned into something else follows different rules. Pesto is basil suspended in oil, and the oil protects the volatiles for a while, but a long bake still dulls both the smell and the colour. Spread it as the base sauce and it will darken. Add it in the last minute of the bake or spoon it over the finished pizza and it stays bright. The basil pesto pairings on this site assume the second approach.
Dried basil is a different ingredient with a different aromatic profile, closer to hay and mint than to the fresh leaf. It belongs in the tomato sauce, where it has time and moisture to bloom, and it does nothing useful sprinkled on top at the end.
Basil oil, made by blanching leaves and blending them with oil, is the trick for getting basil flavour across a whole pizza without a single leaf on it. Blanching locks in the colour: where raw basil in oil turns brown within hours, blanched basil oil stays vivid green for days in the fridge. Drizzle it over the hot pie. It survives contact with the cheese far better than a leaf does, and it reaches the edges of the crust where a torn leaf never lands.
Storage, washing and the mistakes that cost you the leaf
Basil is damaged by cold. Leaves kept in a fridge blacken within a day or two, so a bunch is better standing in a glass of water on the counter with a bag loosely over the top. Buy it the day you need it where you can.
Wash the leaves and dry them properly before use, because wet basil steams instead of wilting and drops water onto the cheese. A salad spinner followed by a gentle blot on a clean towel gets the surface dry enough.
The two habits that ruin basil most often are chopping it early and adding it too soon. A pile of chopped basil sitting on a board while you build the pizza is already oxidising. Leave the leaves whole in a bowl until the last possible moment.
Tonight's margherita
A traditional margherita needs only tomato, mozzarella, basil and olive oil.
Build the pie with sauce and torn mozzarella, slide a few whole oiled leaves under the cheese, and keep the rest of the bunch aside. Bake it hot. Slice it, then tear eight or ten fresh leaves over the top while the surface is still bubbling and finish with a thread of olive oil.
You will get both versions on one pizza, the cooked basil running through the cheese and the raw basil hitting you as you pick up a slice. The caprese pesto pizza and the rest of the herby fresh pizzas use the same timing. After one bake it will be obvious which version you want more of, and every pizza after that one will be better for it.