Preheat the oven to 375ºF. Position an oven rack to the center position.
Whisk the eggs and milk together in a small bowl and set aside.
Heat the olive oil in a large(12-inch) cast-iron skillet or oven-safe pan over medium-high heat. Add the onions and cook for 2 minutes, until they start to soften. Add the garlic and cook until fragrant, about 30 seconds to 1 minute. Mix in the chopped Swiss chard stems and pepper, and sauté them for 2 minutes. Add the Swiss chard leaves and cook them until they start to wilt, about 1 to 2 minutes. Add the grated zucchini, oregano, thyme and salt. Stir to combine.
Turn off the heat. Pour the egg and milk mixture into the skillet. Sprinkle the cheese over the eggs and vegetables. Stir everything to make sure that the vegetables are evenly distributed. Bake the casserole for about 25 to 28 minutes, until the cheese starts to brown.
Remove the casserole from the oven and allow it to cool for a few minutes before slicing it into wedges.
If you do not have a cast-iron skillet, you can bake everything inside a greased 9x9 inch casserole dish. Pour the sautéed vegetables into the dish and then add the eggs and cheese. Use a wooden spoon to stir the vegetables and cheese so that they’re distributed evenly. The cooking time should be roughly the same.