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Keep reading to learn how to make these egg muffins and all the tips for properly packing them in a school lunchbox.

Ham and Cheese Egg Muffins
These ham and cheese egg muffins are perfect for school lunch, breakfast, or to enjoy as a high-protein snack! They come together easily in a bowl with basic staples you always have on hand.
It’s an epic meal prep ingredient you can bake the night before and store in the fridge for 3 days to fill lunch containers. Kids can enjoy them at room temperature or warm in a thermos.
Pack them with fresh fruit, veggies, and your favorite lunch sides for a tasty bento box that’s nutritious and fun to eat!
Ingredients
Open the fridge and you’ll find the simple ingredients that make this Ham and Cheese Egg Muffins recipe come true. Check the list:
- Ham: adds flavor and protein.
- Eggs: give the muffins a fluffy and soft texture while adding protein.
- Plain Greek Yogurt: or any plain yogurt.
- Milk: your favorite.
- Shredded cheese: any variety of Cheddar, mozzarella, Colby Jack, Mexican cheese blend, pepper Jack, or Swiss.
- Salt & pepper: for seasoning.
How to Make Ham and Cheese Lunch Bites
Mix everything in a bowl, fill the muffin pan, and bake: making these Ham and Cheese Egg Muffins couldn’t be any easier! Here’s the simple step-by-step:
- Prep
Preheat the oven to 350F and grease a 24-count mini muffin pan. If using a regular muffin pan, cooking time will vary. - Mix the ingredients
In a large bowl, whisk the eggs, yogurt, and milk. Add ham, cheese, salt, and pepper. Mix to combine. - Fill the muffin pan
Distribute the egg mixture evenly into the muffin pan cups, filling them about ¾ of the way up. - Bake
Bake in the preheated oven for 15-18 minutes. Using a regular-sized muffin tray (yields 12), baking time goes from approximately 26 to 28 minutes. - Remove
Remove the pan from the oven and let them cool in the pan before carefully removing them with a small knife or small spatula. - Refrigerate
Once cooled, refrigerate the ham and cheese egg muffins in an airtight container or zip bag for up to 3 days.
Should Egg Muffins be Eaten Warm, Cold or at Room Temperature?
There’s no right or wrong temperature to enjoy ham and cheese egg muffins. You can eat them cold straight out of the fridge, at room temperature when packed in a lunchbox, or warm from a thermos.
How to Pack Ham and Cheese Egg Muffins in a Thermos
To enjoy these egg muffins warm at lunch, you’ll need to heat them up and place them inside a thermos container. While they won’t be as hot as out of the oven or microwave, they’ll remain warm.
How to store Ham & Cheese Bites
Once the ham and cheese egg muffins are out of the oven and have cooled down to room temperature, remove them from the muffin tray. Then, transfer the egg muffins inside a zip bag or an airtight container and refrigerate for up to 3 days.
How Long Do Egg Muffins Stay Fresh in the Fridge
Egg muffins are the perfect lunchbox builder ingredient you can make ahead and keep in the fridge for up to 3 days.
How to Pack Ham and Cheese Egg Muffins for Lunch
If your kids prefer to enjoy these egg muffins warm, place them in a thermos container. If they don’t mind eating them at room temperature, you can pack them in a regular lunch container. Here’s how to do both:
- To enjoy these at room temperature, place 4 to 6 egg muffins inside the main compartment of a lunch container.
- To eat warm, heat the ham and cheese egg muffins in the microwave for 1 minute, stopping the microwave halfway through to flip them over. Immediately transfer them inside a thermos container and close the lid.
- Finish packing this lunch by adding fruit, veggies, and any other sides inside a bento box. Pack everything inside a lunch bag.
Tips for Packing Ham and Cheese Egg Muffins for Lunch
Here is how I packed these egg muffins in the lunchbox so they stay fresh for hours:
Use a sturdy container
Pack these egg muffins in a thermos or a compartmentalized lunchbox so they will remain intact until lunchtime.
Separate wet from dry ingredients
Place the ham and cheese egg muffins in the main compartment of the lunchbox. If adding crunchy crackers, chips, or nuts, keep them in a different compartment so they won’t absorb any moisture.
Cook once, eat many times
These egg muffins last 3 days in the fridge, making this recipe perfect for meal prep. Once cooked, use them to pack bento box lunches, breakfast on the go, or epic snack boxes.
Related: Top 5 Lunchboxes We’ve Tested
Ham and Cheese Egg Muffins

Ingredients
For the egg muffins:
- ½ cup ham, diced
- 6 eggs
- ¼ cup plain Greek yogurt
- 3 tablespoons milk
- 1 cup shredded cheddar
- ¼ teaspoon salt
- ¼ teaspoon pepper
For each lunch:
- 4-6 egg muffins
- Fruit & veggies
- Lunch sides
Instructions
- Preheat the oven to 350F and grease a 24-count mini muffin pan. See the note below regarding cooking time if using a regular muffin pan.
- In a large bowl, whisk eggs, plain Greek yogurt, and milk. Add ham, cheese, salt and pepper.
- Distribute the egg mixture evenly into the muffin pan cups, filling them about ¾ of the way up.
- Bake in the preheated oven for 15-18 minutes. Remove the pan from the oven and let them cool in the pan before carefully removing them with a small knife or small spatula.
- Once cooled, refrigerate the egg muffins in an airtight container or zip bag for up to 3 days.
For lunch:
- To enjoy these at room temperature, place 4 to 6 egg muffins inside the main compartment of a lunch container.
- To eat warm, heat the egg muffins in the microwave for 1 minute, stopping the microwave halfway through to flip them over. Immediately transfer them inside a thermos container and close the lid.
- Finish packing this lunch by adding fruit, veggies, and any other sides inside a bento box. Pack everything inside a lunch bag.
Barbara says
What do you do for the quiches not to stick to the pan? Mine stick all the time and don’t come out as nice as yours.
MOMables says
Do you use non-stick spray? You can also try muffin liners.
Stacy says
Can these be made in advance and frozen?
MOMables says
Absolutely.
Lees says
How long can they be frozen for?
MOMables says
I’d say up to 1-2 months. Just make sure to defrost them properly!
Tabitha says
I assume you use the milk while you are whisking the egg along with the Greek yogurt
MOMables says
Exactly. Sorry Tabitha!