In a large skillet with a lid, heat olive oil over medium-low heat. Add in garlic and red pepper flakes, cook for 2 minutes or until garlic begins to soften.
Add in mushrooms, tomatoes, salt and pepper. Cook for 5 minutes, or until mushrooms begin to release their water.
Add in spinach and cover skillet. Let spinach wilt for 2 minutes. Remove lid, and stir in the pasta sauce. Remove the skillet from heat and let rest for 5 minutes.
Stir in the Greek yogurt, and then add the pene. Stir until sauce is mixed well and all pasta and veggies are coated. Heat until just warmed through. Divide into pasta bowls and serve topped with parmesan cheese.