Preheat the oven. Set your oven to 375°F (190°C) and line a muffin tin with paper cups or grease with olive oil.
Mix the wet ingredients. In a large bowl, whisk together eggs, olive oil, and milk until smooth and slightly frothy.
Add the flavor base. Stir in chopped garlic, jalapeño slices (reserve a few for topping), bell pepper, thyme, salt, black pepper, nutmeg, and chili flakes.
Incorporate the dry ingredients. In another bowl, combine flour, baking powder, and sugar. Gradually add this to the wet mixture, stirring gently until just combined. Avoid overmixing — a few lumps are fine!
Fold in the cheddar. Add shredded cheddar cheese and fold it evenly through the batter.
Fill the muffin cups. Spoon the batter evenly into muffin tins, filling each about ¾ full. Top with extra jalapeño rounds and a sprinkle of Parmesan cheese.
Bake. Place in the oven and bake for 22–25 minutes, or until golden on top and a toothpick inserted in the center comes out clean.
Cool and enjoy. Let muffins cool slightly before removing from the tin. Serve warm with butter or as a savory side.