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

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

4.28 stars average
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 minutes
COOK: 30 minutes
TOTAL: 35 minutes
Servings: 12 muffins

Recipe Video


  • 1 dozen large eggs
  • ½ cup whole milk
  • 6 slices Candian bacon (diced)
  • ¼ cup minced scallions
  • 4 ounces shredded sharp cheddar cheese (low fat)
  • salt and pepper to taste


  • 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

94 thoughts on “Ham and Cheese Baked Egg Cups”

  1. I made these for my daughter’s grad party and they were a huge hit!!! I experimented with different tricks for getting them out of the pan. Parchment paper muffin liners were perfect and came out flawlessly.
    I also tried other ingredients – broccoli and bacos (fake bacon bits). Easy!
    Thanks for an awesome recipe and my new go to easy breakfast at home or for groups.

    1. How did that work for your grad party? How far ahead did you make these?
      Did you reheat mass amounts in the oven?

  2. Hi, I want to make these but I only have light tan colored stoneware muffin tin. Do I cook at a lower heat for longer or do any modification with the temp and cooking time? Could I grease the stoneware with butter or avocado oil cooking spray? Thanks!

  3. I am making these for a Bridal Shower Brunch…can I make them the night before and ‘re-heat’ in the oven the morning of the shower?

  4. This recipe is fantastic! I’ve been making these for a while now!!
    Just recently, I’ve had them still taste great but not come out of the tub well – breaking a part and such! Any tips or suggestions?

      1. Question:
        The directions say to top the cups with the cheese, yet the video shows adding the cheese to the egg mixture and pouring it into muffin cups. Which is better?

    1. Gisele Chartrand

      I tweek it a bit. Put some ham and left over cooked chicken added some cinnamon. I don’t use salt when I cook only when I bake. It turned out pretty good.

  5. I had leftover ham from Easter and wanted to make egg cups. Found your recipe, doubled to freeze some, and they are delicious—thank you! ????

  6. It’s excellent, but makes WAY MORE than 12 cups. I got 12 very large cups with 4 eggs. I’ll be shocked to see how many cups a full 12 eggs makes.

          1. Yes, I scanned the bar code with an app and they came up 70… not sure where I got the 78. But still puts two muffins over 140 if there’s one egg in each… do/could you make more than 12 with the dozen eggs?

  7. I have made these using ham, cheese, salt, and pepper. Then made them using sausage. I don’t use any peppers or onions since my husband eats very early. I let them cool then wrap 2 together and put in fridge. All he has to do is microwave and fix toast or warm a biscuit. He has really enjoyed having these.
    I froze a few to see how it works. I took 4 out of the freezer last night and he ate them the morning. Not sure how they were but they looked fine last night. I also made a dozen and took to a family with some other foods that had sickness.

    1. Bringing these to friends or neighbors who are ill or in crisis is a great idea!! Keeps a healthy breakfast or snack available. I know from experience there are only so many pans of lasagna you can fit in the freezer!

  8. I’m dairy free. Think would still be good with just the whole eggs, ham, and the Daiya cheddar? We don’t use milk to make our scrambled eggs any longer, either. Thoughts?

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