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These ham and cheese breakfast muffins are a great make-ahead breakfast full of healthy and filling ingredients. Make up a batch of these egg bites on the weekend and enjoy them for grab-and-go breakfasts throughout the week.

breakfast egg muffins with ham and cheese

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If your mornings are busy, and breakfast is often an afterthought, then these ham and cheese egg muffins may just change everything!

Perfect for breakfast meal prep, these egg bites are a tasty and healthy option to start the day right. Simple to make and full of tasty ingredients, cook up a big batch and enjoy them throughout the week.

These healthy breakfast muffins will help you keep on track with a balanced lifestyle and will keep you filling full till lunchtime.

Be sure to try my Easy Breakfast Egg Muffins and Baked Eggs too!

Why you will love this breakfast muffins recipe!

Easy to make: It’s so simple to make up a big batch of these healthy egg muffins and they come out so light and fluffy.
Make ahead: These are so great to make ahead of time. The whole family love them, and you can easily double the recipe to make a big batch for everyone to enjoy throughout the week.
Healthy: Made with fresh veggies, these egg bites are low carb and high in protein. They’ll keep you feeling satisfied and will give you the energy to face the day.

close up image of breakfast muffins with ham and cheese

Ingredients for Egg Muffins with Ham and Cheese

Bell Peppers: I like to use one green and one red bell pepper, but you can use any colors you like.
Onion: Finely chopped and softened before being baked with the other ingredients.
Ham: This is a great recipe if you have leftover ham to use up. It adds a great flavor as well as a boost of protein.
Eggs: Use fresh eggs for this recipe. Check that they are good to use by placing them in a bowl of water. If they aren’t fresh they will float to the top and should be discarded.
Milk: These egg bites can be made with any plant based or dairy milk.
Cheese: Shredded cheese makes these breakfast egg muffins cups super tasty. Any shredded cheese will work well.
Salt and pepper.

ingredients for breakfast egg muffins with ham and cheese

How to make ham and cheese breakfast muffins

Preheat the oven to 375 F and line a muffin tin with silicone muffin molds.
Heat the olive oil in a large skillet over medium heat. Add the onion and cook for about 2 minutes until it starts to soften.
Add the chopped bell peppers and season with salt and pepper. Stir everything together and cook for about 5 minutes until the onions start to brown.
Add ham to the skillet and toss to combine.
Fill each muffin mold with the mixture so that each is filled to about 3/4 full.
In a medium mixing bowl, crack the eggs and add milk. Lightly whisk the eggs and milk but don’t overbeat them if you want to have fluffy mini egg muffins.
Pour about 3 tablespoons of the whisked eggs into each muffin cup, equally distributing among the cups. Fill to the top but be careful not to overfill each muffin cup.
Top each cup with about 1 Tbsp shredded cheese each.
Bake for about 20 minutes, or until breakfast muffins are set and cooked through, and are lightly golden. Allow muffins to cool in the pan on top of a wire rack for about 5 minutes before removing.

process images of breakfast muffins with ham and cheese

How long do they keep?

These breakfast egg muffins are perfect for breakfast meal prep as they will easily keep for up to a week. Once cooled, keep them in an airtight container in the fridge. You can enjoy them cold or heat them for 30 seconds in the microwave to enjoy warm.

Can you freeze them?

Yes, so be sure to make a big batch! Once fully cooled, the keto egg cups can be frozen solid on a baking sheet and then transferred to a container or freezer bag. Thaw them in the fridge overnight before reheating or enjoying cold.

Recipe Variations

It’s easy to make these ham and cheese savory breakfast muffins your own! Add in other fresh veggies like mushrooms, or add in a bit of minced garlic. Sautéed spinach also makes a great addition. You can also mix up the seasonings using dried herbs or spices like paprika or red chili flakes.

TIPS FROM NELI’S KITCHEN

Recipe Notes and Tips

Silicone muffin molds are great to use for this recipe as the egg bites are easy to remove. You can make them straight in a muffin tin, but be sure to oil it well before adding the ingredients.
Don’t over beat the egg and milk mixture. If you do, they won’t rise as much when they are baked.
If making ahead, let the ham and cheese breakfast muffins cool completely before storing.

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