Preheat oven to 400°. Coat an 8x8-inch ovenproof baking dish with nonstick spray.
Cook shells in a pot of boiling salted water just until pliable, 8-9 minutes. Rinse shells with cold water; drain.
For the sauce, sweat onion in oil in a saute pan over medium heat until softened, 3-5 minutes. Add tomato paste, garlic and Italian seasoning; cook until fragrant, 1 minute.
Stir in tomatoes; cook until heated through, 2-3 minutes. Season sauce with salt and black pepper.Cover bottom of prepared dish with a third of the sauce.
For the filling, combine chicken, pesto, mozzarella, ricotta, parmesan, zest and peper flakes; season with salt.
Stuff each shell with a heaping 1 Tbsp filling and arrange in prepared dish, cheese side up. Pour remaining sauce over shells.
Sprinkle mozzarella and parmesan over top of shells. Bake shells until beginning to brown, 25-30 minutes.
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