Preheat the oven to 450˚. Pat the chicken dry with paper towels and season generously with salt and pepper. Arrange skin-side down in a large ovenproof skillet (the chicken will be snug) and place over medium-high heat. Cook until the chicken skin is sizzling, about 5 minutes. Reduce the heat to medium and cook until the skin is very browned and crisp, 8 to 10 minutes (reduce the heat slightly if the chicken is browning too quickly). Transfer the chicken skin-side up to a plate; reserve the skillet.
Meanwhile, remove the lemon zest in wide strips using a vegetable peeler, then juice the lemon. Trim and quarter the shallots. Smash the garlic. Cut the peaches and plums into 3/4-inch-thick wedges.
Discard all but about 1 tablespoon fat from the skillet. Add the lemon zest, shallots and garlic and cook, stirring, until softened, 2 minutes. Add the lemon juice, scraping up any bits from the bottom of the skillet. Add the peaches, plums, honey and thyme sprigs, season with salt and pepper and stir to combine.
Place the chicken, skin-side up, on top of the fruit and transfer the skillet to the oven. Roast until the chicken is cooked through and the fruit is soft and bubbling, about 15 minutes. Discard the thyme sprigs. Divide among plates and top with the thyme leaves.