Ham and Cheese Baked Egg Cups

4.27 stars average

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Ham and cheese baked egg cups are the ideal, protein-packed low carb breakfast recipe 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 two busy kids in school, 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 ingredients, 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).
  • Switch the ham. Canadian bacon is great, but bacon bits or sliced luncheon meat both work great as well.
  • 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

4.27 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
Servings12 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.

Last Step:

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Calories: 108kcalCarbohydrates: 1.2gProtein: 10.4gFat: 5.9gSaturated Fat: 2.1gPolyunsaturated Fat: 3.8gCholesterol: 190mgSodium: 188mgFiber: 0.1gSugar: 0.1g
Did You Make This Recipe?Post a pic and mention @thelemonbowl or tag #thelemonbowl!

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94 responses to “Ham and Cheese Baked Egg Cups”

  1. carina Avatar

    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. Liz DellaCroce Avatar
      Liz DellaCroce

      Ahhh did you use large eggs?

  2. Kaydawn Avatar

    Can this be used with fat free milk?

    1. Liz DellaCroce Avatar
      Liz DellaCroce


  3. morris Avatar

    Are the nutritional facts based on the smaller muffin tins or the larger one?

    1. Liz DellaCroce Avatar
      Liz DellaCroce


  4. Maureen Avatar

    I wanted to make these right away and didn’t have Canadian bacon, so I used DeliSelect ham and they turned out ok.

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      Oh what a great swap out! So glad you enjoyed them!

  5. Megan @ Skinny Fitalicious Avatar
    Megan @ Skinny Fitalicious

    Can never say no to a good egg muffin for breakfast. Protein!

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      I mean honestly! :)

  6. Aimee Avatar

    Hello! Just wondering if the calorie count is for one or
    two egg muffins?
    I can’t wait to try!!

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      It’s for two! :)

      1. Rebekah Avatar

        Isn’t one egg 78 calories itself? Am I misunderstanding that each cup has one egg? I’m trying either way!! ????

        1. Liz DellaCroce Avatar
          Liz DellaCroce

          It depends on the egg, the organic eggs I had for breakfast today just had 60 but some have 70. I’ve never seen an egg with 78 calories though. :) Are you using large?

          1. Rebekah Avatar

            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?

          2. Liz DellaCroce Avatar
            Liz DellaCroce

            Just use 10 eggs. :)

  7. julie lindberg Avatar
    julie lindberg

    Do you really have to pre-cook the veggies? It seems like they would cook enough in 25-30 minutes.

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      You know I’ve never tried it other wise – if you do, please report back!

  8. Charlotte Moore Avatar
    Charlotte Moore

    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. Liz DellaCroce Avatar
      Liz DellaCroce

      I’m so glad you enjoyed these Charlotte! So nice of you to gift them to others as well!

    2. kate roselund Avatar
      kate roselund

      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!

  9. lori Avatar

    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?

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      Yes that would work!

    2. lara Avatar

      i use unsweetened cashew milk in place of dairy in cooking. it has body but no undesirable flavor. also makes great gravy

      1. Liz DellaCroce Avatar
        Liz DellaCroce

        Great idea! Water works too and then you don’t have the calories of cashew milk. :)

  10. Kristi Rimkus Avatar
    Kristi Rimkus

    I saw this recipe over on Google+ and had to stop by. I love these mini egg cups. They offer perfect portion control for us weight watching folks.

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      Oh I’m so glad you said hi!! Yes I’m working on the last 10 pounds so egg cups have been hugely helpful!