Optional Add-Ins
You can also add:
- Diced bell peppers
- Chopped spinach
- Mushrooms
- Broccoli
- Cooked bacon
- Cooked sausage
- Diced tomatoes
- Jalapeños
- Feta cheese
- Monterey Jack
- Mozzarella
Just don't overload the cups with watery vegetables, or the egg mixture can become less firm.
Necessary Kitchen Tools
You won't need much.
- 12-cup muffin pan
- Large mixing bowl
- Whisk
- Measuring cups and spoons
- Cutting board
- Knife
- Spoon or small ladle
- Cooling rack
A silicone muffin pan can also make removal particularly easy.
Ingredient Substitutions
Use a Different Cheese
Cheddar is my favorite here, but you can easily substitute:
- Monterey Jack
- Colby Jack
- Mozzarella
- Swiss
- Pepper Jack
- Gruyère
Want more flavor?
Try a combination of sharp cheddar and Parmesan.
Swap the Ham
Cooked bacon, breakfast sausage, turkey sausage, or leftover roasted chicken can all work.
Just make sure any meat you're adding is already cooked.
Make Them More Vegetable-Heavy
Spinach, mushrooms, peppers, broccoli, and green onions are excellent choices.
For vegetables with a lot of moisture, sauté them first and let them cool slightly before adding them to the egg mixture.
How to Make Low-Carb Ham and Cheese Egg Bakes
Step 1: Preheat the Oven
Preheat your oven to 375°F (190°C).
Lightly grease a 12-cup muffin pan with cooking spray or butter.
Don't skip the greasing!
Eggs have a habit of sticking when given the opportunity.
Step 2: Prepare the Egg Mixture
Crack the eggs into a large bowl.
Add the milk or heavy cream, garlic powder, black pepper, and salt.
Whisk until everything is well combined.
You don't need to whip the eggs excessively. Just make sure the yolks and whites are fully blended.
Step 3: Add the Ham and Cheese
Stir in the diced ham, shredded cheddar, and green onions if using.
Give everything a gentle mix.
Step 4: Fill the Muffin Cups
Divide the mixture evenly among the prepared muffin cups.
Fill each one about three-quarters full.
Don't fill them completely to the top because the eggs will puff up as they bake.
Step 5: Bake
Place the muffin pan in the preheated oven.
Bake for about 18–22 minutes, or until the egg centers are set and the tops are lightly golden.
The egg bakes will puff up beautifully while they're in the oven.
Don't worry if they deflate slightly as they cool.
That's completely normal.
Step 6: Cool and Serve
Let the egg bakes cool in the pan for about 5 minutes.
Run a small knife or spatula around the edges if necessary, then gently remove them.
Serve warm.
And if you're meal prepping, let them cool completely before storing.
How to Tell When They're Done
The centers should look set rather than wet or liquid.
You can also insert a knife into the center of one egg bake. It should come out mostly clean.
For food safety, egg dishes should be cooked until the eggs are fully set. If you're using a thermometer, an internal temperature of 160°F (71°C) is a useful benchmark for dishes containing eggs.
What to Serve With Ham and Cheese Egg Bakes
These little egg cups are satisfying on their own, but there are plenty of ways to turn them into a bigger breakfast.
Try serving them with:
- Fresh berries
- Avocado slices
- Fresh fruit
- Tomato slices
- Sautéed spinach
- Roasted vegetables
- A simple green salad
- Low-carb toast or bread, if desired
For brunch, arrange them on a platter with fresh herbs and colorful vegetables.
They look much fancier than the amount of effort involved!
Tips for the Best Egg Bakes
Grease the Pan Well
This is probably the most important tip.
Eggs can cling stubbornly to muffin pans.
Don't Overbake
Overbaked eggs can become rubbery.
Take them out as soon as the centers are set.
Chop the Ham Small
Small pieces distribute more evenly, giving you ham in nearly every bite.
Use Freshly Shredded Cheese
Freshly shredded cheese generally melts more smoothly than some pre-shredded varieties.
Don't Overfill the Cups
Leave room for the eggs to puff as they bake.
Let Them Rest
A few minutes of cooling makes them easier to remove from the pan.
Can I Make These Ahead of Time?
Absolutely!
That's one of the biggest reasons to love this recipe.
Bake a batch ahead of time, allow them to cool completely, and refrigerate them in an airtight container.
When you're ready for breakfast, simply reheat the number you need.
It's such a nice feeling to open the refrigerator and realize breakfast is already waiting for you.
How to Store Low-Carb Egg Bakes
Store cooled egg bakes in an airtight container in the refrigerator for up to 3–4 days.
Place parchment between layers if you want to prevent them from sticking together.
How to Reheat
Microwave one or two egg bakes for about 20–40 seconds, depending on your microwave.
For several at once, you can reheat them gently in a 300°F oven until warmed through.
Avoid overheating them, since eggs can become rubbery when reheated too aggressively.
Can You Freeze Egg Bakes?
Yes!
Let them cool completely first.
Wrap individual egg bakes or place them in a freezer-safe container or bag.
Freeze for up to about 2 months for best quality.
Thaw overnight in the refrigerator, then reheat.
You can also reheat them from frozen, although the texture may be slightly different.
Easy Flavor Variations
Once you've made these once, you'll probably start thinking about all the other combinations you can try.
Ham, Spinach and Swiss
Use Swiss cheese and add a handful of sautéed spinach.
Ham and Pepper Jack
Pepper Jack gives these a little kick.
Bacon and Cheddar
Replace the ham with cooked, crumbled bacon.
Classic for a reason!
Mushroom and Gruyère
Sauté chopped mushrooms before adding them to the egg mixture, then use Gruyère for a rich, savory variation.
Southwest Style
Add diced peppers, a little cumin, cooked sausage, and Pepper Jack.
Top with fresh cilantro after baking.
Frequently Asked Questions
Are these egg bakes keto-friendly?
They can fit into many low-carbohydrate eating plans, but the exact carbohydrate content depends on the ingredients you use, particularly the ham and any additions. Check the nutrition information on your specific products if carbohydrate limits are important to you.
Can I use heavy cream instead of milk?
Yes. Heavy cream will make the egg bakes richer and creamier. You can also use half-and-half.
Why did my egg bakes shrink after baking?
That's normal.
Eggs naturally puff as they cook, then settle as they cool. A little shrinking doesn't mean anything went wrong.
Why are my egg muffins watery?
Excess moisture can come from vegetables such as spinach, mushrooms, tomatoes, or zucchini.
Sauté watery vegetables first and drain them well before adding them.
Can I use leftover ham?
Absolutely. In fact, this is a perfect recipe for leftover cooked ham.
Just dice it into small pieces before adding it.
Can I make these without milk?
Yes.
The milk adds tenderness, but you can leave it out if necessary. The texture may be slightly firmer.
Can I use silicone muffin cups?
Yes. Silicone liners or a silicone muffin pan can make removing the egg bakes easier.
Are these good for meal prep?
Definitely. They're one of those breakfasts that were practically made for meal prep.
Bake once, refrigerate, and reheat throughout the week.
General Recipe Information
Prep Time: 10 minutes
Cook Time: 18–22 minutes
Total Time: About 30–35 minutes
Servings: 12 egg bakes
Cuisine: American-inspired
Category: Breakfast / Brunch
Difficulty: Easy
Final Thoughts
If breakfast has to be quick in your house, these Low-Carb Ham and Cheese Egg Bakes deserve a spot in your regular rotation.
They're simple.
They're cheesy.
They're packed with savory ham.
And they're ready to grab whenever hunger strikes.
I especially love that you can make them ahead of time and change the ingredients depending on what's hanging around in the refrigerator.
A little spinach here.
Some leftover bacon there.
Maybe Pepper Jack instead of cheddar.
Before you know it, you've got a completely different breakfast.
Easy, filling, customizable, and wonderfully cheesy—what's not to love?!
If you make these, leave a review and tell me what you added. And don't forget to share a photo on Pinterest—I always love seeing how readers make these recipes their own!
Approximate Nutrition
Nutrition will vary depending on the type of ham, cheese, milk, and optional ingredients used.
Estimated per egg bake:
- Calories: 110–140
- Protein: 9–11 g
- Fat: 7–10 g
- Carbohydrates: 1–3 g
- Fiber: 0–1 g
- Sugar: 0–1 g
- Sodium: 300–450 mg
For the most accurate nutrition information, calculate the recipe using the exact brands and quantities you use.
