Place a rack in the center of your oven and preheat the oven to 400 degrees F. Generously coat a large rimmed baking sheet with nonstick spray.
Place the cherry tomatoes and red onion in a large bowl. Add 2 tablespoons pesto, 1/4 teaspoon kosher salt, and ¼ teaspoon black pepper. Toss to coat, then spread into a single layer on the prepared baking sheet.
Bake the tomatoes and onion for 10 minutes, then remove from the oven and with a spatula, stir them around a little to promote even cooking, then return to the oven for 10 additional minutes.
Meanwhile, pat the salmon fillets dry. Sprinkle with ½ teaspoon salt and 1/4 teaspoon black pepper. Spread 1 tablespoon of the remaining pesto over each fillet.
Rub the pesto on with your fingers or the back of a small spoon as needed. Make sure each fillet is completely covered in pesto.
Remove the sheet pan from the oven and move the tomatoes and onions to the outsides to make space for the salmon in the center. Arrange the salmon fillets down the center of the baking sheet, skin-side down.
Return the pan to the oven and bake the pesto salmon until the fish flakes easily with a fork and reaches an internal temperature of 145 degrees F, about 16 to 20 minutes.*
Sprinkle the salmon with a pinch of additional kosher salt and squeeze lemon over the top. Top with fresh basil as desired. Enjoy!
*The cooking time will vary based upon the thickness of your salmon. Thicker (2-inch-plus) slices will need several extra minutes, while thinner slices may cook more quickly.
TO STORE: Refrigerate salmon and vegetables in an airtight storage container for up to 2 days.
TO REHEAT: Gently rewarm leftovers on a baking sheet in the oven at 350 degrees F.