Preheat oven to 400 degrees F. Coat four 10-ounce ovenproof ramekins with cooking spray and place on a baking sheet. Heat oil in a large nonstick skillet over medium-high heat. Add potatoes, brussels sprouts, onion and garlic and cook, stirring, until softened and beginning to brown, about 6 minutes. Divide the mixture among the prepared ramekins.
Whisk egg substitute, cheese, milk, thyme, salt and pepper in a medium bowl. Pour the egg mixture over the potato mixture and gently stir to combine.
Transfer to baking sheet to the oven. Bake until the eggs are set and an instant-read thermometer inseted in a frittata registers 160 F., about 25 minutes