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Breakfast Egg Muffin Cups (3 Ways!)

If you love meal prep breakfasts that are quick, healthy, and endlessly customizable, these Breakfast Egg Muffin Cups are going to be your new favorite.
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Prep Time 10 minutes
Cook Time 25 minutes
Servings: 6
Course: Appetizer, Breakfast, Snack
Cuisine: American
Ingredients Method Notes

Ingredients
  

  • 10 large eggs – the base of the muffins.
  • ½ cup milk – dairy or unsweetened plant-based milk works.
  • ½ tsp garlic powder – adds subtle flavor.
  • ¼ tsp onion powder – optional but gives depth.
  • Salt & black pepper to taste
  • 1 cup shredded cheese – cheddar Swiss, mozzarella, or your favorite.
  • Fillings of choice – bacon ham, spinach, tomatoes, bell peppers, onions, mushrooms, etc.
  • Fresh herbs optional – parsley, chives, or thyme for brightness.
  • Filling Ideas 3 Delicious Combos
  • Bacon + Cheddar + Parsley
  • Ham + Swiss + Chives
  • Spinach + Cherry Tomatoes + Mozzarella

Method
 

  1. Preheat the oven to 350°F (175°C). Grease a 12-cup muffin tin generously with nonstick spray.
  2. Whisk the eggs. In a large bowl, whisk together eggs, milk, garlic powder, onion powder, salt, and pepper until well combined.
  3. Add the fillings. Divide your chosen meats, veggies, and cheese evenly among the muffin cups.
  4. Pour the egg mixture. Carefully pour the whisked eggs into each cup, filling about halfway to ¾ full (they will puff up while baking).
  5. Bake. Place the muffin tin in the oven and bake for 22–24 minutes, or until the eggs are set and no longer jiggly in the center.
  6. Cool slightly. Let them rest in the pan for 5 minutes before removing. This helps prevent deflating and makes them easier to handle.

Notes

Spray generously: Nonstick spray is key to easy release. If your muffin tin is older, consider using a ceramic-coated pan or parchment liners.
Chop small: Dice veggies and meats into small pieces so every bite is balanced.
Partially cook hearty veggies: Potatoes, carrots, or beets should be pre-cooked before adding.
Cool before storing: Prevents excess condensation in your container.
Flavor boost: Try Italian seasoning, paprika, or a drizzle of hot sauce before serving.
Storage & Meal Prep
Fridge: Store in an airtight container for up to 4 days.
Freezer: Wrap individually in parchment paper and freeze in a zip-top bag for up to 2 months.
Reheat: Microwave 30–45 seconds straight from the fridge (or 1–2 minutes from frozen).
Serving Ideas
These egg muffin cups are versatile and can be enjoyed on their own or paired with:
A side of avocado or toast for a more filling breakfast.
Fresh fruit for a balanced plate.
Salsa, hot sauce, or sriracha for a spicy kick.