Cook the pasta in a large pot of salted boiling water according to package directions until al dente. Just before draining, reserve about 1 cup of the pasta water.
While the pasta cooks, heat the olive oil in a large skillet or Dutch oven over medium-high heat. Add the sliced sausage and chopped shallot.
Cook, stirring occasionally, until the sausage is browned and the shallot is soft, about 4-5 minutes. The sausage is pre-cooked, but ensure it is heated through to an internal temperature of 165°F (74°C).
Add the chopped apple, minced garlic, red pepper flakes (if using), salt, and pepper to the skillet. Cook for 5 minutes, stirring occasionally, until the apple is tender-crisp.
Pour in the chicken broth to deglaze the pan, scraping up any browned bits from the bottom. Add the rinsed beans and fresh spinach. Stir until the spinach has wilted, about 1-2 minutes.
Drain the pasta and add it directly to the skillet with the sausage and apple mixture. Add the Parmesan cheese and toss everything together to combine.
Add a splash of the reserved pasta water (starting with 1/4 cup) to the skillet, stirring until a light sauce forms that coats the pasta. Add more water as needed to reach your preferred consistency.
Serve immediately, topped with additional grated Parmesan cheese if you like.