Pat the chicken thigh chunks dry with paper towels, then season them generously with salt, pepper, onion powder, garlic powder, and thyme. Let the seasoned chicken sit at room temperature for 15 minutes while you fill a large pot with salted water and bring it to a rolling boil—this allows the flavors to penetrate the meat and also gives you time to get other prep work done.
While the water heats and chicken seasons, thinly slice the mushrooms into 1/4-inch pieces, finely dice the onion, and mince the fresh garlic. Once the water is boiling, add the fettuccine and cook for 8-10 minutes until al dente. Drain the pasta in a colander and set aside—I like to reserve about 1/4 cup of pasta water to loosen the sauce later if needed.
Heat 2 tablespoons of olive oil in a large skillet over medium-high heat until shimmering. Add the seasoned chicken chunks and cook for 12-15 minutes, stirring occasionally, until golden brown on all sides and cooked through. Transfer the chicken to a clean bowl. In the same skillet with the remaining oil, add the sliced mushrooms and sauté for 4-5 minutes until they release their moisture and begin to brown. Move the mushrooms to another bowl.
In the same skillet, melt 1 tablespoon of butter over medium heat. Add the finely diced onion and minced garlic from Step 2 and cook for 3 minutes, stirring frequently, until softened and fragrant. Sprinkle the flour over the mixture and stir constantly for 1-2 minutes to create a roux—this acts as a thickener for the sauce. Gradually pour in the chicken stock, milk, and cream while whisking to prevent lumps from forming.
Bring the sauce to a gentle simmer and cook for 2-3 minutes, stirring occasionally, until it thickens slightly. Add the italian seasoning, freshly grated nutmeg, and red pepper flakes, then taste and adjust salt and pepper as needed. I find the nutmeg adds a subtle warmth that elevates the whole dish, so don't skip it even though it's a small amount.
Remove the skillet from heat and add the cooked fettuccine from Step 2 and the sautéed mushrooms from Step 3, gently folding them into the sauce. Add the seared chicken from Step 3 back into the skillet and fold everything together until well combined. Sprinkle the freshly shredded parmesan cheese over the top and gently stir until the cheese melts into the sauce, creating a silky coating. If the sauce seems too thick, add a splash of the reserved pasta water to reach your desired consistency.
Divide the chicken thigh fettuccine alfredo among serving bowls or plates. Garnish each portion with fresh parsley and a crack of black pepper to add a pop of color and flavor contrast.