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.

In this Post: Everything you need for 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!
Ingredients
- 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

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

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

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

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

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

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

Finish by sprinkling each cup with shredded cheese.

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

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.

More Easy Breakfasts
- Make-Ahead Fruit and Yogurt Parfaits
- Almond Flour Berry Muffins
- Asparagus and Goat Cheese Frittata
- Overnight Mixed Berry French Toast Bake
- Make-Ahead Smoothie Freezer Bags
Did you try this recipe and like it? The next time you make it, snap a picture and share it to your socials! Tag @thelemonbowl and #thelemonbowl so we can admire and share your dish.

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
Recipe Video
Ingredients
- 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
Instructions
- 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.
Made them without milk and they were AMAZING!
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.
Love the idea of broccoli and bacon!!
How did that work for your grad party? How far ahead did you make these?
Did you reheat mass amounts in the oven?
Mine stuck to the pan really bad even with spraying. Any tips?
Hmm is it a non-stick pan? That always helps too!
Can you use semi skimmed milk or do you have to use whole milk??
Can you use semi skimmed milk instead of whole??
Yes absolutely!!
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!
Same cook time I believe! Maybe try a few minutes less then cook until firm on top?
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?
Yes definitely!!!
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?
Oh interesting. Are you spraying the pan?
How many of the egg muffins is one serving?
One :)
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?
Both are the same. :)
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.
Oooo that sounds so good!
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! ????
Oh perfect I’m so glad!!
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.
Ahhh did you use large eggs?
Can this be used with fat free milk?
YES!
Are the nutritional facts based on the smaller muffin tins or the larger one?
Regular!
I wanted to make these right away and didn’t have Canadian bacon, so I used DeliSelect ham and they turned out ok.
Oh what a great swap out! So glad you enjoyed them!
Can never say no to a good egg muffin for breakfast. Protein!
I mean honestly! :)
Hello! Just wondering if the calorie count is for one or
two egg muffins?
I can’t wait to try!!
It’s for two! :)
Isn’t one egg 78 calories itself? Am I misunderstanding that each cup has one egg? I’m trying either way!! ????
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?
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?
Just use 10 eggs. :)
Do you really have to pre-cook the veggies? It seems like they would cook enough in 25-30 minutes.
You know I’ve never tried it other wise – if you do, please report back!
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.
I’m so glad you enjoyed these Charlotte! So nice of you to gift them to others as well!
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!
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?
Yes that would work!
i use unsweetened cashew milk in place of dairy in cooking. it has body but no undesirable flavor. also makes great gravy
Great idea! Water works too and then you don’t have the calories of cashew milk. :)
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.
Oh I’m so glad you said hi!! Yes I’m working on the last 10 pounds so egg cups have been hugely helpful!