Heat 1 tablespoon of the oil in a medium saucepan over medium-high heat.
Add the quinoa and toast, stirring occasionally, for 4 minutes. Add the water, reduce the heat to low, and simmer for 15 minutes, or until the quinoa is tender. Drain off any remaining water.
Meanwhile, add the remaining 1 tablespoon oil to a large skillet over medium heat. Add the onion and garlic and cook, stirring frequently, for 5 minutes, or until the onion softens.
Add the Swiss chard and cook, stirring frequently, for 4 minutes, or until wilted. Add the tomato and cook until heated through.
Fold in the quinoa, stirring well to combine. Add the pepper flakes and cheese. Season to taste with salt and pepper. Stir again. Let stand for 3 to 5 minutes to blend the flavors.