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Preheat the oven to 375 degrees F. Lightly coat a 9x13-inch baking dish with nonstick spray.
In a large skillet, heat the olive oil over medium high. Once the oil is hot and shimmering, add the diced chicken. Sprinkle with salt and pepper. Sauté the chicken until golden on all sides and fully cooked through, about 4 minutes. Remove to a plate and set aside.
In a large stockpot of boiling, generously salted water, cook the pasta to al dente according to package instructions. Reserve 1 cup of the pasta cooking liquid, then drain. Return pasta to the stockpot.
While the pasta cooks, in a small bowl, whisk together the pesto and Greek yogurt until evenly combined.
Stir in the spinach, breaking it up as needed and stirring until evenly combined.
To the stockpot with the pasta, add the pesto/Greek yogurt mixture. Gently stir to coat the noodles in the pesto mixture. If the sauce is too thick, splash in some of the pasta water. It should be a little saucy.
Add the cooked chicken, cherry tomatoes, and red pepper flakes. Gently toss to combine.
Pour half of the pasta into the prepared baking dish. Sprinkle evenly with 1/2 cup mozzarella and half of the basil. Layer the remaining half of the pasta over the top, spreading it into an even layer. Sprinkle with the remaining 1/2 cup mozzarella.
Bake for 20-25 minutes until the cheese is melted and just barely starts to turn golden. Remove and sprinkle immediately with the Parmesan cheese and fresh basil. Serve warm.