Prep the pan: Heat the oven to 350°F (175°C). Lightly grease a 12-cup muffin tin with nonstick spray, or use parchment liners. Grease the liners too to prevent sticking.
Sauté aromatics: Warm olive oil in a small skillet over medium heat.
Add onion and a pinch of salt. Cook 3–4 minutes until soft and translucent. Add garlic and cook 30 seconds until fragrant.
Remove from heat and cool briefly.
Chop the veggies: Finely chop spinach so it distributes evenly. Quarter cherry tomatoes and pat them dry with a paper towel to reduce extra moisture.
Whisk the eggs: In a large bowl, whisk eggs, milk, salt, pepper, and smoked paprika (if using) until smooth and slightly foamy.
Add the mix-ins: Stir in the sautéed onion, spinach, tomatoes, cheese, and herbs. Taste a small drop of the mixture and adjust seasoning if needed.
Fill the cups: Divide the mixture evenly among the muffin cups, filling each about 3/4 full.
Give the tin a gentle tap on the counter to settle the ingredients.
Bake: Bake 16–20 minutes, until the muffins are set and lightly puffed. A toothpick inserted in the center should come out mostly clean.
Cool and release: Let the muffins cool in the pan for 5 minutes. Run a thin knife around edges if needed, then transfer to a cooling rack.
Serve or store: Enjoy warm, or cool completely before refrigerating or freezing.