Preheat oven to 350°F. Spray muffin pan with cooking spray.
Dice onion and mince garlic. Heat oil in skillet; add onion to hot oil and sauté for 3-4 minutes. Add garlic and cook for 1 minute longer. Stir in spinach and cook until it begins to wilt, approximately 2 minutes. Remove from heat and allow to cool.
Whisk eggs together with salt, pepper, parsley, thyme, and chives.
Add feta to each muffin cup. Stir cooled onions into egg mixture and pour over feta.