Preheat the oven to 450°F. Line a baking sheet with parchment paper.
Stretch the dough into a large oval and lay on the baking sheet. Spread the onions over the dough, followed by the shredded smoked fontina and chopped bacon. Sprinkle the black pepper over top and drizzle with olive oil. Place in the oven and bake until crust is golden brown, about 15 minutes.
Remove from the oven and sprinkle the thyme leaves over top. Cut into wedges and serve at once.