Heat the olive oil in a large (12-inch) nonstick skillet over medium-high heat for about 2 minutes.
Add the shallot. Sprinkle them with a pinch of kosher salt and black pepper. Cook, stirring occasionally, until translucent, about 5 minutes. Lower the heat to medium.
While the onion is cooking, whisk the eggs, ½ teaspoon of kosher salt, a pinch of black pepper, and 2 tablespoons of parmesan in a medium bowl. Set aside.
When the onions are golden brown, add the spinach leaves to the skillet. Cook, stirring, just until the leaves begin to wilt, about 1 minute. Don't overcook the spinach.
Pour the egg mixture into the skillet. Cook the eggs over medium heat, pushing them back and forth with a rubber spatula, until set to your liking.
Sprinkle the scramble with red pepper flakes. Serve immediately.
