Crack the 4 large eggs into a medium bowl, add the 1 tablespoon grated Parmesan cheese, and whisk until blended. Add a pinch of sea salt and black pepper and whisk once more; set the egg mixture aside.
Place a nonstick skillet over medium heat and add the 1 tablespoon unsalted butter. Melt the butter until foamy but not browned.
Add the 1 small minced shallot to the skillet and cook, stirring occasionally, for 2–3 minutes until translucent.
Add the 1 minced clove of garlic and cook, stirring, for about 30 seconds until fragrant (do not let it brown).
Add the 2 cups fresh baby spinach leaves to the skillet and cook, stirring, for about 1–2 minutes until the spinach is fully wilted.
Pour the reserved egg and Parmesan mixture evenly over the spinach. Let the eggs sit undisturbed for about 20–30 seconds, until the edges begin to set.
Using a heatproof spatula, gently push and fold the eggs from the edges toward the center, repeating occasionally until the eggs are mostly set but still moist—about 1–2 minutes total. Remove the skillet from the heat when the eggs are slightly underdone; residual heat will finish them.
Transfer the scrambled eggs to a plate and garnish with a pinch of red pepper flakes. Taste and, if desired, add an additional pinch of sea salt and black pepper.