Baked Ham and Cheese Egg Cups

Made with just 3 ingredients, these Baked Ham and Cheese Egg Cups are a quick, healthy and filling breakfast. They’re an easy breakfast on the go and can be made ahead of time, making them perfect for meal prep!

An egg cup cut open with a fork with some toast.

If your home is anything like mine, mornings can be a bit hectic and rushed. I always aim for a balanced breakfast that will keep me full until lunch but the reality is, I just don’t have a lot of time to prepare a big or fancy breakfast this morning. Some days I’m lucky if we all have time to sit down and eat.

That’s where that’s Baked Ham and Cheese Egg Cups come in. Whether I make them fresh in the morning or pull one out of the fridge or freezer, they are a filling breakfast that’s ready in minutes.

Baked egg cups are a bit like an omelette on the go, with all of your favorite omelette ingredients and, I think, even easier to make.

While ideally, I prefer to sit down and enjoy these ham egg cups with a slice of toast as a proper meal, I have also been known to pop one or two in the microwave and eat them in the car on an extra busy day.

The recipe below calls for deli ham and any variety will do but my personal favourite is honey ham. It just adds an extra bit of flavour.

Use this cheese and ham egg cup recipe as a base guideline – if you’re a veggie lover, add in some pepper or onions, switch up the cheese, add a splash of hot sauce for an extra kick or replace the eggs with egg whites if you prefer.

I recommend making a double batch when you bake these and popping the rest in the fridge or freezer for those mornings when there just isn’t time to do anything else!

Ingredients & Substitutions

  • Eggs – if you want, you can substitute just egg whites
  • Sliced Deli Ham – make sure it’s not super thinly sliced. Honey ham has a great flavour but I also sometimes use black forest.
  • Shredded Cheese – I recommend a mix of cheddar and mozzarella but any cheese will work!
  • Salt and Pepper – to taste
  • Green Onions – optional, for a bit of flavour and colour or chives if you have them.

How To Make Cheese and Ham Egg Cups

These ham egg cups are beyond simple to make.

Preheat your oven to 350 degrees.

Line each muffin cup with a slice of deli ham.

Add a pinch of cheese. You want to use approximately 1/2 of your cheese in this step.

Crack an egg into the centre of each ham egg cup and sprinkle with salt and pepper.

Bake for 10 minutes.

Remove from the oven and add a pinch of cheese to each baked egg cup.

Return to the oven for an additional 3-5 minutes.

How long should I bake cheese and ham egg cups?

Bake time will depend on how you prefer your eggs. If you like them a little runny, 13 minutes is perfect but if you want them fully cooked, keep them in the oven for the full 15 minutes.

How To Store Baked Egg Cups:

As I mentioned, these ham and cheese egg cups are perfect for meal prep because they store so well.

After baking, allow them to cool completely before placing in an airtight container or Ziploc.

These will last in the fridge for 4 days and the freezer for up to 1 month. To reheat, just pop in the microwave at 30-second intervals.

A baked egg cup topped with green onions with a side of toast

Baked Ham and Cheese Egg Cups

Alisa Infanti | The Delicious Spoon
Baked egg cups are a quick, easy and healthy breakfast!
5 from 6 votes
Prep Time 5 mins
Cook Time 15 mins
Total Time 20 mins
Course 21 Day Fix, Breakfast, Lunch, Snack
Cuisine North American
Servings 6 servings
Calories 250 kcal


  • Oven
  • Muffin Tin
  • Measuring Spoons


  • 12 eggs
  • 12 slices deli ham
  • 1 cup shredded cheddar and mozzarella cheese mix
  • salt and pepper to taste
  • sliced green onions (optional)


  • Preheat oven to 350F
  • Add one slice of ham to each muffin cup
  • Add a pinch of cheese in each cup (1/2 the cheese)
  • Carefully crack an egg into the centre of each ham lined muffin cup
  • Sprinkle with salt and pepper
  • Bake for 10 minutes
  • Add a pinch of cheese to the top of eggs (remaining cheese)
  • Bake another 3-5 minutes 


Serving: 2egg cupsCalories: 250kcalCarbohydrates: 1.4gProtein: 23.4gFat: 16.3gSaturated Fat: 6.7gPolyunsaturated Fat: 2.1gMonounsaturated Fat: 5.7gTrans Fat: 0.3gCholesterol: 365mgSodium: 1028mgPotassium: 362mgFiber: 0gSugar: 0.4gVitamin A: 663IUVitamin C: 0mgCalcium: 179mgIron: 1.9mg


If following the 21 Day Fix Container System this recipe counts for approx:
2 red, 1 blue
Please Note:

The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice.

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  1. 5 stars
    This is such a lovely breakfast idea for my boys. I must make them this tomorrow morning. I bet they gonna love it. Thanks for the idea and the recipe.

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