Ham and Cheese Baked Egg Cups

Ham and cheese baked egg cups are the ideal, protein-packed low carb breakfast that can be made ahead in a muffin tin and quickly reheated on busy weekday mornings.

Liz cutting ham and cheese baked egg cups.

With school starting back up, it’s safe to say that our mornings are a little hectic. While many mornings I start my day with a smoothie, these make-ahead Ham and Cheese Baked Egg Cups have been a total game-changer when it comes to having something healthy and delicious ready for my kids and husband. Versatile and quick, with healthy and balanced gredients, these baked egg cups are a no-brainer for you and your family!


  • Eggs: A great way to get protein in the morning, they are also chalk full of other vitamins and minerals.
  • Milk: I used whole milk for the added fat content, but you could use whatever you have.
  • Ham: I used canadian bacon, but you could use leftover baked ham, sliced deli meat, or whatever else you have on hand!
  • Scallions: Also called green onions, they add a fresh, bright flavor to the eggs.
  • Cheese: Sharp cheddar cheese adds great salty, pungent, and (big surprise) sharp flavor to the eggs. But again, any cheese you have would add to the flavor of the dish.

How to make Ham and Cheese Baked Egg Cups

Spraying muffin tin with baking spray

Prepare for your Ham and Cheese Baked Egg Cups by preheating your oven to 350 and spraying your muffin tin with cooking spray.

Cutting ham

Then cut your ham into small, bite-sized pieces, and mince your scallions.

Cracking eggs into bowl

Next in a large bowl, carefully crack your dozen eggs.

Whisking milk into eggs

Beat your eggs with a whisk, and slowly stir in your milk. Season with a pinch of salt and pepper.

adding scallion to egg

Then add in the minced scallions and diced ham. Stir to make sure it’s evenly incorporated.

Pouring egg mixture into muffin tin

Then using a ladle or measuring cup, evenly distribute the egg mixture into your muffin tin.

Sprinkling cheese on top of egg cups

Finish by sprinkling each cup with shredded cheese.

Baked ham and cheese egg cups

Bake your egg cups for about 25-30 minutes, or until eggs are set.

Ham and cheese baked egg cups garnished with scallions.

Remove from the oven and let cool before removing from the muffin pan. Then store for easy breakfasts later, or garnish with additional scallions to enjoy right away!

Switch It Up

  • Make it vegetarian. Take the ham out of the equation, and this becomes vegetarian (though not vegan).
  • Change up the vegetables. Throw in whatever you have! Corn, spinach, and bell peppers are other options I’ve tried.

Frequently Asked Questions:

How long do egg cups keep for?

If saving to eat later in the week, let cool completely before storing in an airtight container. These egg cups will keep in the fridge for up to 5 days.

How long should egg cups be reheated for?

Reheat in the microwave for 60 seconds if refrigerated, 2-3 minutes if frozen.

Can you put eggs in paper muffin cups?

Yes you can! I would still spray the pan with cooking spray though.

Ham and cheese baked egg cups.

More Easy Breakfasts

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Liz enjoying ham and cheese baked egg cups.

Get creative and make these your own! These Ham and Cheese Baked Egg Cups are a great way to use up veggies, or let your kids customize what they like!

Your fork is waiting.

Ham and cheese baked egg cups 2

Ham and Cheese Baked Egg Cups

Ham and cheese baked egg cups are the ideal, protein-packed breakfast that can be made ahead in a muffin tin and quickly reheated on busy weekday mornings.

PREP: 5 mins

COOK: 30 mins

TOTAL: 35 mins


Servings: 12 muffins

  • Pre-heat oven to 350 degrees and spray a muffin pan with cooking spray or use a silicone pan.
  • In a large bowl, whisk together eggs and milk until light and fluffy. Stir in the Canadian bacon, scallions and salt/pepper to taste.

  • Divide egg mixture evenly between 12 muffin tins (about 1/3 cup each) then sprinkle evenly with sharp cheddar.

  • Bake until eggs are set, 25-30 minutes. Let cool slightly to ensure eggs are set before removing from pan to serve.

Calories: 108kcalCarbohydrates: 1.2gProtein: 10.4gFat: 5.9gSaturated Fat: 2.1gPolyunsaturated Fat: 3.8gCholesterol: 190mgSodium: 188mgFiber: 0.1gSugar: 0.1g