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Preheat your oven to 375°F. Bring a large pot of salted water to a rolling boil. Add the penne pasta and cook according to package directions until al dente, about 8-10 minutes. Drain the pasta well and set aside.
While the pasta cooks, heat the olive oil in a large Dutch oven or deep skillet over medium heat. Add the chopped yellow onion and cook until softened and translucent, about 5-7 minutes.
Add the minced garlic to the skillet and cook for 1 minute more until fragrant, being careful not to burn it.
Stir in the crushed tomatoes, dried oregano, red pepper flakes (if using), salt, and black pepper. Bring the sauce to a gentle simmer, then reduce the heat to low and let it cook for 10 minutes, allowing the flavors to meld.
Remove the sauce from the heat and stir in the heavy cream and fresh chopped basil until well combined.
Add the drained penne pasta to the sauce in the Dutch oven or skillet. Add 1 1/2 cups of the shredded mozzarella cheese and 1/4 cup of the grated Parmesan cheese. Stir everything together until the pasta is evenly coated and the cheeses are melted.
Transfer the pasta mixture to a 9x13 inch baking dish. Sprinkle the remaining 1/2 cup of shredded mozzarella cheese and 1/4 cup of grated Parmesan cheese evenly over the top.
Bake in the preheated oven for 20-25 minutes, or until the cheese is melted, bubbly, and lightly golden brown on top.
Remove the pasta bake from the oven and let it rest for 5-10 minutes before serving. This allows the sauce to set and makes for easier serving.

Preheat your oven to 375°F. Bring a large pot of salted water to a rolling boil. Add the penne pasta and cook according to package directions until al dente, about 8-10 minutes. Drain the pasta well and set aside.
While the pasta cooks, heat the olive oil in a large Dutch oven or deep skillet over medium heat. Add the chopped yellow onion and cook until softened and translucent, about 5-7 minutes.
Add the minced garlic to the skillet and cook for 1 minute more until fragrant, being careful not to burn it.
Stir in the crushed tomatoes, dried oregano, red pepper flakes (if using), salt, and black pepper. Bring the sauce to a gentle simmer, then reduce the heat to low and let it cook for 10 minutes, allowing the flavors to meld.
Remove the sauce from the heat and stir in the heavy cream and fresh chopped basil until well combined.
Add the drained penne pasta to the sauce in the Dutch oven or skillet. Add 1 1/2 cups of the shredded mozzarella cheese and 1/4 cup of the grated Parmesan cheese. Stir everything together until the pasta is evenly coated and the cheeses are melted.
Transfer the pasta mixture to a 9x13 inch baking dish. Sprinkle the remaining 1/2 cup of shredded mozzarella cheese and 1/4 cup of grated Parmesan cheese evenly over the top.
Bake in the preheated oven for 20-25 minutes, or until the cheese is melted, bubbly, and lightly golden brown on top.
Remove the pasta bake from the oven and let it rest for 5-10 minutes before serving. This allows the sauce to set and makes for easier serving.