These Egg Casserole in Muffin Cups are a delicious, protein-packed breakfast you can take on the go. Each fluffy mini casserole is loaded with eggs, cheese, and your favorite veggies or breakfast meats. They’re baked in a muffin tin for perfectly portioned servings that are ideal for meal prep or quick weekday mornings. Warm, satisfying, and customizable — this recipe makes breakfast easy and fun.
Table of Contents

Egg Casserole in Muffin Cups
- Total Time: 32 minutes
- Yield: 12 muffins 1x
Description
These Egg Casserole in Muffin Cups are a delicious, protein-packed breakfast you can take on the go. Each fluffy mini casserole is loaded with eggs, cheese, and your favorite veggies or breakfast meats. They’re baked in a muffin tin for perfectly portioned servings that are ideal for meal prep or quick weekday mornings. Warm, satisfying, and customizable — this recipe makes breakfast easy and fun.
Ingredients
- 8 large eggs
- ½ cup milk (whole or 2%)
- ½ cup shredded cheddar cheese (or your favorite)
- ½ cup diced bell peppers
- ¼ cup chopped onions
- ½ cup cooked and crumbled bacon or sausage
- ½ tsp salt
- ¼ tsp black pepper
- Cooking spray or butter (for greasing the muffin tin)
Instructions
- Preheat the oven: Set to 375°F (190°C). Grease a 12-cup muffin pan generously with cooking spray or butter.
- Prepare the egg mixture: In a large mixing bowl, whisk together eggs, milk, salt, and pepper until smooth.
- Add fillings: Stir in cheese, vegetables, and cooked meat of choice.
- Fill muffin cups: Divide the mixture evenly among the muffin cups, filling each about ¾ full.
- Bake: Bake for 18–22 minutes, or until the tops are set and lightly golden.
- Cool and serve: Let cool for a few minutes before removing from the pan. Serve warm or store for later.
Notes
Veggie options: Try spinach, mushrooms, or diced tomatoes. Cheese swaps: Monterey Jack, feta, or pepper jack work well. Make it spicy with jalapeños or red pepper flakes. Dairy-free option: Use almond milk and skip the cheese or use a dairy-free alternative. Storage: Refrigerate up to 5 days or freeze up to 2 months. Reheat in microwave 30–40 seconds or oven 5 minutes at 350°F.
- Prep Time: 10 minutes
- Cook Time: 22 minutes
- Category: Breakfast
- Method: Baked
- Cuisine: American
Nutrition
- Serving Size: 1 muffin
- Calories: 120
- Sugar: 1g
- Sodium: 260mg
- Fat: 9g
- Saturated Fat: 4g
- Unsaturated Fat: 4g
- Trans Fat: 0g
- Carbohydrates: 1g
- Fiber: 0g
- Protein: 8g
- Cholesterol: 110mg
Keywords: egg casserole, muffin cups, breakfast, high protein, meal prep
Why You’ll Love It
- Grab-and-go breakfast: Perfect for busy mornings or lunchboxes.
- Customizable: Add your favorite ingredients — cheese, veggies, or bacon.
- Protein-rich: Each muffin delivers a solid boost of morning energy.
- Freezer-friendly: Reheat quickly for a no-stress breakfast.
If you’re looking for more easy morning inspiration, check out our Breakfast Protein Biscuits or these hearty California Chicken Breakfast Burritos.

Ingredients
- 8 large eggs
- ½ cup milk (whole or 2%)
- ½ cup shredded cheddar cheese (or your favorite)
- ½ cup diced bell peppers
- ¼ cup chopped onions
- ½ cup cooked and crumbled bacon or sausage
- ½ tsp salt
- ¼ tsp black pepper
- Cooking spray or butter (for greasing the muffin tin)
Instructions
- Preheat the oven: Set to 375°F (190°C). Grease a 12-cup muffin pan generously with cooking spray or butter.
- Prepare the egg mixture: In a large mixing bowl, whisk together eggs, milk, salt, and pepper until smooth.
- Add fillings: Stir in cheese, vegetables, and cooked meat of choice.
- Fill muffin cups: Divide the mixture evenly among the muffin cups, filling each about ¾ full.
- Bake: Bake for 18–22 minutes, or until the tops are set and lightly golden.
- Cool and serve: Let cool for a few minutes before removing from the pan. Serve warm or store for later.
Tips & Variations
- Veggie options: Try spinach, mushrooms, or diced tomatoes for extra color and flavor.
- Cheese swaps: Monterey Jack, feta, or pepper jack all work well.
- Make it spicy: Add jalapeños or a sprinkle of crushed red pepper flakes.
- Dairy-free option: Use almond milk and skip the cheese or use a dairy-free alternative.
Pair these egg muffins with a side of Crispy Air Fryer Breakfast Potatoes or a refreshing glass of Carrot Juice for a balanced morning meal.
Storage & Reheating
- Refrigerate: Store in an airtight container for up to 5 days.
- Freeze: Place cooled muffins in a freezer bag and freeze for up to 2 months.
- Reheat: Microwave for 30–40 seconds or warm in a 350°F oven for 5 minutes.
FAQs
Can I make these ahead of time?
Absolutely! These egg muffins are great for meal prep. Store in the fridge or freezer for an easy breakfast all week.
Can I use egg whites only?
Yes, substitute 1 cup of liquid egg whites for every 4 whole eggs. The muffins will be lighter but still delicious.
Why did my muffins deflate?
They may deflate slightly as they cool — that’s normal. For fluffier results, whisk air into the eggs before baking.
More to Try
Conclusion
Egg Casserole in Muffin Cups are the perfect breakfast solution — wholesome, easy to customize, and simple to store. Whether you’re feeding a crowd or prepping for the week, these little egg bites will make mornings smoother and more satisfying. Try them once, and they’ll become a staple in your breakfast rotation!