Preheat oven to 190°C (375°F). Grease all 12 muffin cups generously including the sides and rim.
Sauté diced onion in olive oil over medium heat for 4–5 minutes until soft.
Add garlic and cook 1 minute until fragrant.
Add spinach and stir until wilted, 1–2 minutes. Season lightly. Remove from heat.
Transfer spinach mixture to paper towels. Press firmly to squeeze out all moisture.
Whisk eggs, milk, salt, pepper, garlic powder, oregano, and red pepper flakes for a full minute until smooth and airy.
Stir squeezed spinach, half the feta, Parmesan, parsley, and dill into the egg mixture.
Pour evenly into prepared muffin cups, filling each three-quarters full.
Scatter remaining feta over the top of each muffin.
Bake 18–22 minutes until puffed, golden at the edges, and set in the center.
Cool in the tin for 5 minutes before running a knife around the edges to loosen.
Remove carefully and serve warm or cool completely before storing.