Ham and Cheese Egg Muffins

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Ham and Cheese Egg Muffins make an easy, portable, and healthy breakfast that's packed with protein, good-for-you, and taste amazing.


Egg Muffins with ham, tomatoes, spinach, and plenty of cheddar cheese should immediately be added to your weekly menu for a grab and go breakfast everyone will love.

I have a slight obsession with eggs muffins and make them almost weekly for quick breakfasts and snacks.

Truth be told, I probably eat this more often as a post-workout snack than I do for breakfast. They are also a great way to clean out your fridge since you can pretty much toss anything in and they will taste delicious.

Like many of my egg muffin recipes, this version was created late on Sunday as I was preparing for the week ahead. After a quick revision of the fridge, I immediately knew I needed to use up some leftover deli ham.

Since a grilled ham, cheese, and tomato is one of my favorite sandwiches, I used that for inspiration and made an egg muffin with the same delicious ingredients, plus some spinach for greens. Within ten minutes they were in the oven and within 30 minutes, I had breakfast and snacks prepped for the week.

How to make egg muffins?

Egg muffins or mini quiche are one of my favorite things to make for quick and easy breakfasts. Here is the basic recipe for making egg muffins:

  • 12 eggs
  • 1 cup fillings (cooked veggies, lean protein, deli meats, herbs, beans, etc.)
  • 1/2 cup cheese (shredded or crumbled)
  • Salt and pepper (plus any other spices you like)
  • Directions: Preheat the oven to 350 degrees. Spray the muffin tin with cooking spray. Whisk the eggs until combined. Season with salt and pepper. Add the fillings. Divide evenly among the muffin tin. Bake for 20-25 minutes until cooked through. Wait 5-10 minutes before removing them from the tin.

Egg muffins with ham, cheese, tomatoes, and spinach in a muffin tin and with ingredients on the side.

Can you freeze egg cups?

Egg muffins freeze really well. To freeze these ham and cheese egg muffins, start by letting the muffins cool completely. Then place them on a baking sheet and let them freeze for a couple of hours. They should feel froze on the outside. Next, you can individually wrap them or add them to a freezer safe bag.

To reheat, wrap the egg muffin in a damp paper towel and microwave for 15-30 seconds until heated through. Depending on the strength of the microwave this could vary.

How long do they last in the fridge?

Egg muffins will last 4-5 days in the fridge in an airtight container. They can be eaten cold, at room temperature, or can be microwaved. If you find your egg muffins get dry in the microwave, you can wrap them in a moist paper towel before placing them in the microwave.

It's important to note that egg muffins will deflate but after coming out of the oven, but they still taste delicious.

Recipe Ideas for Ham and Cheese Egg Muffins

There are so many ways to customize these egg muffins and make them your own.

  • Make the spicy: Add some spice with chopped fresh or pickled jalapeno peppers. You can also use red pepper flakes or some drained pico de gallo in place of the tomatoes.
  • Add beans: For some added fiber, add some black beans or chickpeas.
  • Use egg whites: For a lighter option, use egg whites in place of whole eggs. You could also use a combination of the two.
  • Swap in new vegetables: If you don't love spinach, use chopped broccoli instead. You could also use zucchini or cauliflower.
  • Different proteins: Experiment with different kinds of ham. Honey ham will add some sweetness. Black forest ham has more smoke. Chopped ham will have more texture. You could also use center cut bacon, turkey bacon, or sausage.
  • Add mushrooms: Sauté some mushrooms and throw them in as well to add some earthy flavors.

Tips and Tricks

Some people have trouble cooking egg muffins. Follow these tips so they turn out great every time.

  • Cook vegetables first: You can use absolutely any combination of veggies you like in these muffins. Personally, I like to cook most veggies (tomatoes are the exception) before adding them to the egg muffins. I think it makes for a better texture.
  • Add different meat and cheese: Just like the veggies, you can switch up the deli meat and cheese. Turkey and even roast beef turn out great as do pretty much any variety of cheese you like.
  • Cool before storing: If possible, let these cool completely before refrigerating them. I find they keep the best this way and don't get soggy from the extra moisture that's released as they cool.

Sous Vide Egg Muffins in an Instant Pot

If you love the soft sous vide egg bites from Starbucks, you can create an egg muffin with a similar texture using an Instant Pot.

Start by adding about 1 cup of water to the bottom of the Instant Pot and add the steamer trivet. Then pour the eggs into a silicone egg bite mold. Cover with foil and carefully place in the Instant Pot.

Then cook on the "Steam" setting for 10 minutes. Let the pressure naturally release and carefully remove them from the mold.

Frequently Asked Questions

Here are the most common questions about making egg muffins.

There are a few things that can make egg muffins rubbery. The first is cooking them too long. If the eggs are overcooked, they can get tough. Then when they are reheated that toughness becomes rubbery. 

Another reason is storing them in the fridge while they are still hot. Always let them cool to room temperature before storing them in the fridge. 

Silicone muffin tins and egg molds are the bets options for egg muffins since they are completely nonstick. Egg muffins normally stick to traditional muffin tins, no matter how much cooking spray is used.

The Recipe
Egg Muffins with ham and cheese in a muffin tin.

Ham and Cheese Egg Muffins

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  • 8 eggs
  • 4 egg whites
  • 1/2 tbsp Dijon mustard (optional)
  • Salt and pepper to taste
  • 4 oz. deli ham, chopped
  • 3/4 cup reduced fat shredded cheddar cheese
  • 1/2 cup tomatoes, chopped
  • 1/2 cup frozen spinach (defrosted and squeezed of extra moisture, or cooked fresh spinach)
  • 2 green onions, chopped

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Preheat the oven to 350 degrees.


Whisk together the eggs, egg whites, mustard, salt, and pepper. Stir in the ham, cheese, spinach, tomatoes, and green onions.


Spray a standard muffin tin with cooking spray or line with paper liners. Pour in the egg mixture and bake for 12-14 minutes until cooked through and puffy.

Nutritional Facts
Serving Size: 2 muffins
Amount Per Serving
Calories 168
Calories from Fat 73
% Daily Value *
Total Fat 8g
Saturated Fat 3g
Monounsaturated Fat 0g
Polyunsaturated Fat 0g
Cholesterol 262mg
Sodium 506mg
Total Carbohydrate 3g
Dietary Fiber 1g
Sugars 2g
Protein 19g

* Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.

The Nutritional Values provided are estimates only and may vary based on the preparation method.


If you don't alter the servings, this recipe makes 12 standard size muffins.
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About the author Meet Kristen McCaffrey
Hi, I’m the cookbook author, recipe developer, and food enthusiast behind Slender Kitchen. I am obsessed with making healthy food that is easy to prepare and absolutely delicious. Meal planning is my secret weapon and I hope I can make meal time easier for you with our tried and tested recipes and foolproof meal plans. Learn More
On Ham and Cheese Egg Muffins
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Jennifer Black
February 20, 2024 - 09:48
Add a Rating:
Hi Kristen! Thanks for adding the question about rubbery muffins. I experienced this issue with my last batch. The taste fine, just so chewy! I'll try your tips. Also, I wonder if adding milk or cottage cheese helps? I typically just use a 100% egg mixture, but maybe adding some dairy will help ward off the rubber. Thoughts?
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November 24, 2020 - 20:58
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November 25, 2020 - 13:18
It's for 12 muffins! Updated the recipe now to make that more clear. Thanks!
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Christina Jayroe
October 30, 2018 - 16:08
Can you freeze these? If so, any special instructions?
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Ana Sanchez
March 19, 2018 - 20:47
Add a Rating:
So good. I seem to be making these every week on Sunday and eating them Monday - Thursday. :-) Last week I tried using my mom's sous vide. Very easy and adaptable.
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November 29, 2017 - 13:08
Add a Rating:
Very good. Prep time is more like 15 min if you are starting fresh cutting and cooking broccoli.
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