Mix the dough: In a large bowl, whisk flour, salt, and sugar.
Stir in yeast. Add warm water and 2 tablespoons olive oil. Mix with a spoon until no dry pockets remain.
The dough will be sticky—that’s right.
First rise: Cover the bowl tightly and let it rise at room temperature for 1 to 2 hours, until doubled and bubbly. For deeper flavor, refrigerate up to 24 hours after it starts rising.
Prep the pan: Generously oil a 9x13-inch metal pan or a large cast-iron skillet with 2 to 3 tablespoons olive oil. You want a visible sheen—this is what crisps the bottom.
Shape the dough: Oil your hands and scrape the dough into the pan.
Gently stretch it toward the edges. If it resists, let it rest 10 minutes, then stretch again.
Second rise: Cover loosely and let it rise 30 to 45 minutes, until puffy and relaxed. Preheat your oven to 425°F (220°C) while it rests.
Dimple and top: Drizzle 1 to 2 tablespoons olive oil over the dough.
With oiled fingertips, press straight down to create deep dimples across the surface. Sprinkle half the cheddar across the dough. Press in half the jalapeno slices so they sit slightly in the dough.
Add the remaining cheddar and jalapenos on top. Finish with a pinch of flaky salt.
Bake: Bake for 20 to 25 minutes, until the cheese is bubbling and the top is deeply golden. The edges should look fried from the oil.
Optional extra crisp: For a darker bottom, place the pan on the lowest rack for the last 3 to 5 minutes.
Cool and finish: Let it rest in the pan for 10 minutes, then loosen the edges with a spatula and transfer to a rack.
Brush lightly with more olive oil if you like and sprinkle with chives.
Serve: Cut into squares or strips. Best warm, but still great at room temperature.