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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.

    ham and cheese bakes egg cups in a muffin tin

    Everyone warned me that two would be harder than one but boy were they right! To say that our mornings are a little hectic would be an understatement. By the time I nurse the baby, change a zillion diapers and get my 2-year-old to sit down long enough to eat breakfast, I am barely able to take two sips of my coffee. These make-ahead Ham and Egg Cups have been a total game-changer for several reasons:


    Why makes egg cups so good for you?

    Lean: Two of these egg muffins have less than 200 calories and provide over 20 grams of protein! Now that I’m finally back at the gym, protein is even more vital for muscle function.

    Ham and Cheese Baked Egg Cups a healthy gluten free breakfast recipe

    Versatile: When I first made these muffins, I actually made “His and Hers” versions. Since I typically share a green smoothie with my toddler mid-morning, I decided to skip the veggies in mine. For my husband, I quickly sautéed broccoli and kale then placed a little in the bottom of each muffin tin before pouring in the egg mixture.

    Saves Times: These muffins take 5 minutes to whisk together in a bowl before I pop them in the oven to bake. Once they have cooled, I refrigerate them until I need them later in the week. A quick 30-60 seconds in the microwave and a hot and healthy breakfast is done. (PS: My goal in life is to have someone describe me as “hot and healthy.”)

    Ham and Cheese Baked Egg Cups a healthy easy breakfast recipe

    The bottom line: get creative and make these your own with whatever veggies you have on hand that week! These are a great way to use up veggies a little past their prime and avoid food waste. It’s also a great way to let the kids customize their own muffins and have fun in the kitchen.

    What would you put in your egg muffins??

    Your fork is waiting.

    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 5 days.

    How long should egg cups be reheated for?

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

    Why are the cooked egg cups not coming out of the muffin tin?

    Make sure you are spraying the muffin tins with cooking spray.

    ham and cheese bakes egg cups in a muffin tin

    Ham and Cheese Baked Egg Cups

    4.25 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 mins
    COOK: 30 mins
    TOTAL: 35 mins
    Servings: 12 muffins


    • 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.

    Recipe Video


    Calories: 108kcalCarbohydrates: 1.2gProtein: 10.4gFat: 5.9gSaturated Fat: 2.1gPolyunsaturated Fat: 3.8gCholesterol: 190mgSodium: 188mgFiber: 0.1gSugar: 0.1g
    SHOW AND TELL ON INSTAGRAM!Show me your creation and rate it below! Mention @thelemonbowl or tag #thelemonbowl! I would LOVE to see!

    Check out my Pinterest board for more healthy breakfast recipes!


    Liz DellaCroce

    Liz Della Croce is the creator and author of The Lemon Bowl, a healthy food blog. Since 2010, Liz has been sharing delicious recipes that just so happen to be healthy. By using real ingredients with an emphasis on seasonality, Liz has built a growing audience of loyal readers who crave good food for their families.


    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.

    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. 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. 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.

          2. 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! ????

          3. 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?

                  2. 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!

                  3. 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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