Cooking the Pasta
Bring a pot of salted water to a boil and cook 4 ounces whole wheat spaghetti noodles according to package directions until al dente. Reserve a small splash of pasta water, then drain and set aside.
Cooking the Sausage
Heat 1 tablespoon of the 3 tablespoons olive oil (divided) in a large skillet over medium heat. Add 1 pound sweet Italian sausage (bulk or casing removed) and cook for about 5–7 minutes, breaking it apart as it browns, until fully cooked and slightly crisp. Remove from the skillet and set aside.
Building the Vegetable Base
In the same skillet, add another 1 tablespoon olive oil. Add 1 small thinly sliced onion and cook for 3–4 minutes until softened. Stir in 2 cloves minced garlic and cook for about 30 seconds until fragrant. Add 1 cup sliced small sweet peppers and cook for another 3–4 minutes until slightly tender. Stir in 1 cup halved cherry tomatoes and cook for 2–3 minutes until they begin to soften and release their juices.
Combining Everything
Return the cooked sausage to the skillet and add the drained pasta. Drizzle in the remaining 1 tablespoon olive oil and toss everything together. Add the zest and juice of 1 lemon, ½ cup grated Pecorino Romano cheese, black pepper to taste, and ½ teaspoon red pepper flakes (optional). Toss well, adding a splash of reserved pasta water if needed to help create a light, glossy sauce.
Finishing and Serving
Remove from heat and garnish with fresh chopped basil or parsley. Serve immediately with extra Pecorino Romano cheese on top for added flavor.