Pre-heat oven to 375 F.
Place the chicken sausage, shallot, and butternut squash on a sheet pan (do not overcrowd; use two pans if needed). Sprinkle with Italian seasonings and ¼ tsp salt, and drizzle with olive oil. Toss to combine.
Place the sheet pan(s) in the oven and roast for 15 minutes. Remove from the oven and toss the mixture gently.
Return to the oven and roast an additional 10 minutes, or until everything is golden and cooked through.
Lightly grease two, 12-cup muffin tin with cooking spray. Spread a thin layer of parmesan cheese into each individual muffin tin (using just 1/3 cup).
Remove sheet pan(s) from the oven set aside to cool. Turn the heat down to 350 F.
In a large bowl, whisk the eggs together until fluffy. Add paprika and remaining salt and whisk to combine.
Place 1-2 tablespoons of the roasted veggie mixture into each muffin tin.
Pour egg mixture into each muffin cup until it covers the veggie mixture, about halfway full. Sprinkle each cup with the remaining parmesan cheese.
Bake egg muffins for 20-25 minutes or until eggs are set.
Remove from the oven and let cool. Serve warm, or refrigerate in a tightly sealed container for up to 4 days.
Freezer Tip! Make an extra batch to freeze! Place cooked muffins on a baking sheet and place in the freezer for an hour. Wrap each cup with plastic wrap (to avoid freezer burn) and store in a zipper top bag or a tightly sealed container. To reheat, place on a baking sheet in a 375-degree oven for 5-7 minutes, or until fully warmed up. Will stay good in the freezer up to one month.