These egg muffins cups with ham and cheese are light and custardy, so simple to make, easy for meal prep, and perfect for breakfasts on the go.
I don’t think you can have too many easy, high-protein egg-based breakfast recipes up your sleeve. Dishes like my bacon, broccoli, and potato frittata, my healthy homemade Egg McMuffin, and my microwave egg caprese breakfast cups are perfect to eat on your way out the door. These Egg Muffins with Ham and Cheese are yet another recipe to add to your “breakfasts for busy mornings” collection. The inspiration for these egg muffins cups was my ham and cheese breakfast casserole. They have the same texture as an egg strata (an Italian egg and bread casserole, similar to a savory bread pudding) with ham, cheese, and tomatoes added in. The best part about these egg muffins is you can swap out ingredients and make them your own. Plus, you can prep them the night before and bake in the morning in under 30 minutes. Or, bake and reheat for a minute when you’re ready to eat them.
In This Post
Why You’ll Love Them
- Egg Muffins are super customizable—customize them with whatever ingredients you’re craving: red peppers, mushrooms, bacon, sausage, and different cheeses and herbs. It’s your cup and your choice.
- They’re meal prep-friendly
- Egg muffins are protein-rich so they’ll keep you full until lunchtime
Egg Muffins Ingredients
You don’t need many ingredients to make these egg muffins cups. Remember, these are easily customizable too, so feel free to swap out with your favorite flavors. Here’s what you’ll need:
- Eggs—large eggs work best
- Milk–I use whole milk to make the eggs more custardy, but half-and-half or 2% will work
- Dry mustard–this lends a nice, subtle tangy, savory flavor
- Parmesan cheese–Parmesan adds a salty tang and melts into the egg
- Kosher salt and freshly ground black pepper–for seasoning
- Cubed bread–I use sourdough but you french bread or white bread work too
- Tomato–any type you like; or try sun-dried tomatoes
- Ham–I use simple deli ham here, but any kind will do (or try bacon, cooked pancetta, or Canadian bacon
- Fontina cheese–I love the meltiness of this creamy white cheese. You could also use comté, gruyere, Monterey jack, or medium cheddar
- Fresh basil–I like the herbaceousness that basil adds but parsley works too
Find the complete recipe with measurements below.
How to Make Egg Muffins
These egg muffins are so simple to make, everything just needs at least 1 hour and up to overnight to soak and get happy). I love making these at night and letting them hang out in the fridge while I sleep. Then in the morning, poof, all I have to do is turn my oven on!
- Whisk the wet ingredients. In a bowl, whisk milk and dry mustard together until well blended. Add eggs, Parmesan cheese, salt, and pepper.
- Combine the bread and other filling ingredients. In a separate bowl, combine bread, ham, tomato, cheese and basil.
- Prep your pan and bake. In a non-stick large muffin tin or popover pan, spray with cooking spray. Evenly fill the muffin cups with the bread mixture. Pour the egg mixture over the bread mixture until they’re evenly distributed or ⅔ full.
- Refrigerate the muffins for at least one hour or overnight. This helps the egg mixture soak into the bread.
- Bake the muffins. In the morning, take them out of the fridge, preheat the oven to 350°F, and bake for 20-30 minutes until the eggs are set. Let sit in the pan for 5 minutes before removing to eat or save at room temperature or in the fridge.
FAQ and Recipe Tips
- How long does it take to bake egg cups at 350°F? About 20-30 minutes or until your eggs have set and begin to pull away from the sides of the muffin tin.
- Why are my egg cups rubbery? Your egg cups should not be rubbery. If they are, you’ve likely overbaked them.
- Plan ahead. Allow for ample time for the bread to soak up the liquid—at least 1 hour and up to overnight.
Storage Tips
- Egg muffins will keep stored in an airtight container in the fridge for about 4 or 5 days, and in the freezer for about 3 months.
Recipe Additions and Substitutions
- Make these in a 12-cup muffin tin or a 6-cup popover pan.
- Instead of ham, try cooked pancetta or bacon, or chopped Canadian bacon
- Add slivered spinach or kale
- I use whole milk but half-and-half, 2% milk, or plain almond milk works too.
- I use sourdough or French bread but white bread or Texas toast will work
- Instead of fresh tomatoes, try sun-dried tomatoes
- Any other melty cheese works well but you could also try goat cheese or feta cheese
What to Serve With These Egg Muffin Cups
- The Perfect Mimosa
- The Best Bloody Mary
- Berry Delicious Fruit Salad
- Gwyneth’s Blueberry Muffins
- THE BEST Breakfast Potatoes
- The Best Crispy Oven Roasted Potatoes
If you make this recipe, please let me know! Leave a ⭐️⭐️⭐️⭐️⭐️ rating on this recipe below and leave a comment, take a photo and tag me on Instagram with #foodiecrusheats.
Egg Muffin Cups (with Ham and Cheese)
Ingredients
- 4 eggs
- ¼ cup whole milk
- ½ teaspoon dry mustard
- ¼ cup grated Parmesan cheese
- ½ teaspoon kosher salt
- ¼ teaspoon freshly ground black pepper
- 2 ½ cups cubed bread , sourdough, french bread, or white bread
- 1 small tomato , seeded and diced
- 1 cup diced ham , (3 ounces)
- ½ cup fontina cheese , (4 ounces), cut into small cubes
- 2 tablespoons fresh basil , thinly sliced
Instructions
- In a bowl, whisk milk and dry mustard together until well blended. Add eggs, Parmesan cheese, salt, and pepper. In a separate bowl, combine bread, ham, tomato, cheese and basil.
- Spray a non-stick 12-cup muffin tin or 6-cup popover pan with cooking spray. Evenly load each cup with the bread mixture. Whisk the egg mixture again and pour it evenly over the bread mixture or until the cups are ⅔ full. Cover with plastic wrap and refrigerate for at least one hour or overnight.
- When ready to bake, take the tins from the fridge and preheat the oven to 350°F. Bake for 20-30 minutes until the eggs are set and begin to pull away from the sides of the tin. Cool the muffins in the tin for 5 minutes before removing. Enjoy warm, at room temperature, or store in the fridge. The muffins will keep for 3-4 days in the refrigerator.
Notes
Nutrition
More Eggy Breakfast Recipes to Try
- Mediterranean Egg Bites
- Microwave Egg Caprese Breakfast Cups
- Easy Quiche Lorraine
- Mediterranean Breakfast Strata
- Southwestern Vegetable Hash
- Bacon Broccoli and Potato Frittata
- Baked Eggs in Stuffed Peppers
- Ham and Cheese Breakfast Casserole
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Sophia P.
Heidi and her Ham and Cheese Baked Egg Cups are an absolute triumph! From the moment I sunk my teeth into these delectable treats, I was transported to a realm of culinary bliss. The eggs were perfectly fluffy, the ham delightfully savory, and the cheese wonderfully melty—each bite a symphony of flavors that left me yearning for more. But what truly sets Heidi’s creation apart is the sheer genius of its simplicity. With each bite, I found myself marveling at how such humble ingredients could come together to create something so divine. As I savored every mouthful, I couldn’t help but think about how much I want to destroy my husband for devouring the last one without saving me a single bite! Truly a five-star experience that I cannot recommend highly enough.
So glad you enjoyed them Sophia! They are pretty tasty and great for meal prep!
Lesa Cote
I appreciate your expertise in preparing breakfast cups. The baked egg recipe is great.
Annette Comes
Can these be frozen after they are baked and then reheated in microwave like the Jimmy Dean Frittatas?
Thanks
Yes, they certainly could!
Terri
Just popped some into oven! Besides being delicious, there’s next to no carbs in these which we both have to watch!
Sue
I see great possibilities for lightning these up for us dieters. 2% cheese, egg substitute, broken up whole wheat english muffins,low fat milk, etc. Going to make a batch tomorrow! Thank you for all your great ideas. Your web site is marvelous.
Jennifer Weberman (@Dr_Weberman)
I made the “6 Easy Baked Egg Breakfast Cups” for a brunch last weekend and they were mouth watering! I skipped the ham and basil, used Challah bread instead of sourdough and reduced the cheese a small amount and they came out perfect They even reheated well in the microwave the following day. Thank you for sharing!
Yea! I’m so glad to see you adapted the recipe, because you really can turn it into whatever moves you. Thanks for commenting!
Emilia Welch
I might have to throw a baked egg party! I’m not a spinach eater, but those dooooo look tasty enough to try. PS: just curious, am I missing something essential by not refrigerating?
Erin Howard
Heidi, I love the blog and can’t wait to see the magazine! These look delicious and I know everyone in my family would love them (except Addy who will only eat toast…).
Casey
I made your Ham & Cheese Baked Egg Cups with my popover pan yesterday for dinner and they were absolutely fantastic! Also, I didn’t refrigerate them before (because I was so excited to try them and didn’t have the patience) and they were still fantastic! Thanks so much for sharing the recipe! This will definitely be a repeat-offender! I can’t wait to try other ingredients in the egg cups!
Lovin’ your blog,
Casey
PS: just curious, am I missing something essential by not refrigerating? Just curious why that step is in there! thanks so much!
carly {carlyklock}
This is one of my new favorite things to make! Another thing I love about it is that it’s no big deal to make each cup with unique ingredients – now everyone’s happy ! :)
And the versatility. Oh, lordie. Think of the possibilities Carly!! XO
Adrienne
Love this idea! I make a variation of these as biscuits. Such a quick grab and go breakfast!
Oh biscuits would be amazeballs. I need to master my biscuit.
Denise @ TLT
As you can see from my last post: I’m such a cooking/baking-in-cup-lover as well. These recipes have inspired me, as this website always does:) Have a wonderful week!
Oh I love your quiches! Okay, another one to add to my list!
Kulsum at JourneyKitchen
Food in cups is even better than jars! Love it
Pssst…its gonna be the new ‘trend’. :)
Deborah
This comes at a perfect time, because just this morning I was thinking of how bored I am with our go-to breakfasts. Looks like I have some more choices I need to try out!!
Amy
Heidi – This mama shares your love of serving hot breakfasts on a weekday without actually doing any work. mom = rockstar !
Ahhh, Amy. I love you hot mama. Forever 21.
Barbara @ Barbara Bakes
A great way to sneak some veggies in in the morning.
And that is NOT always easy!
Kari
Your egg cups look awesome! Seems like a great & easy alternative to the “egg bake” dish. I will be trying these!
Super easy, super yum.
Rachel
What an awesome collection you’ve put together here! I’m a huge fan of eggs and anything cooked in a muffin tin so obviously I’m in love with these recipes. The English muffin cups and baked potato cups are particularly intriguing. I might have to throw a baked egg party!
Hey, that’s a fun idea. A party with all different baked eggs in cups, then everyone gets a different bite.
Paula @ Dishing the Divine
I don’t love eggs for breakfast (only sweet breakfast for me!) but love them for lunch or dinner. So tasty! These all look delicious! I kind of want to test your spinach theory. :) I’m not a spinach eater, but those dooooo look tasty enough to try. :) and ps – that popover can is *adorable*!
That’s the beauty, breakfast, lunch, dinner. Dessert. Snack. Feast.
Averie @ Love Veggies and Yoga
Heidi these all look amazing! And if I would make ANY of them for my hubs, I could get away with just about anything, espi if I made the Mini Smoked Salmon Quiches. Oh I may try…
:)