Heat a skillet over medium-low heat. Coat with cooking spray or add the olive oil.
Add the diced onion and cook for 2–3 minutes, until softened and translucent. Add the spinach and toss until wilted, about 2 minutes. Remove from the heat and allow the vegetables to cool slightly.
Preheat the oven to 375°F (190°C). Generously coat a 9x13-inch baking pan with cooking spray.
Crack the whole eggs into a medium mixing bowl and add the egg whites. Whisk vigorously for about 30 seconds.
Add the milk, kosher salt, and black pepper. Whisk again until thoroughly combined.
Gently fold the shredded cheddar, sliced cherry tomatoes, and cooled spinach-onion mixture into the eggs.
Pour the mixture evenly into the prepared baking pan. Bake for 25–30 minutes, or until the eggs are completely set in the center.
While the eggs bake, split the English muffins and arrange them cut-side up on a baking sheet. Place them in the oven for about 10 minutes.
After approximately 7 minutes of toasting, place one cheddar slice on each bottom muffin half. Return them to the oven for the final 3 minutes, or until the cheese melts.
Let the baked egg mixture cool for several minutes. Use a round cookie cutter, glass, or jar lid to cut six portions roughly the size of the English muffins. Alternatively, cut the eggs into squares with a knife.
Place one egg portion onto each muffin and close with the cheese-topped half to complete your Healthy Breakfast Sandwich.
Serve warm, or cool completely before storing for meal prep.