Preheat your oven to 375°F. Line six muffin pan cavities with silicone cups and spray them with oil.
In a large spouted measuring cup, whisk together the eggs, black pepper, garlic powder, and red pepper flakes. Using a rubber spatula, mix in the parmesan and scallions.
Fill the prepared muffin cups almost to the edge. The mixture will be liquid (obviously), so I like to use a measuring cup with a spout when pouring.
Top the muffins with the sliced tomatoes, dividing them evenly.
Place the muffin pan on a large baking sheet to catch any spills. Bake until the muffins are set, puffed, and lightly browned, and a toothpick inserted in their center comes out clean, about 20-25 minutes.
Allow the muffins to cool in the pan for a couple of minutes until they are easier to handle, then release them from the silicone cups. Enjoy them immediately, or place them on a cooling rack for 10-15 more minutes before refrigerating them in an airtight container.
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Notes
It's best to bake these muffins in a lightly greased silicone muffin pan. That's the only type of pan that they reliably won't stick to. Another safe option is to use small ceramic ramekins and grease them well.
I don't add any salt because the parmesan adds plenty. But you can add a small amount of salt if you'd like (the nutrition info will obviously change).
The muffins puff up in the oven, then deflate when you take them out. This is normal and expected.
This recipe scales easily. You can double it to make 12 muffins. Keep them in the fridge, in an airtight container, for up to 4 days. Reheat them gently in the microwave at 50% power. Or enjoy them cold!