Ham and Cheese Egg Muffins

Mornings can be chaotic, but breakfast doesn’t have to be. If you’re tired of skipping meals or resorting to sugary cereals, it’s time to introduce egg muffins into your routine. These savory, protein-packed breakfast bites are simple to make, customizable to fit any diet, and perfect for busy mornings when time is short as you can easily meal prep them.

I chose to add ham, cheese and veggies to these egg muffins but there are so many ways to customize this recipe! I started to add some sausage to mine but realized that I had some deli ham that needed to be used before it spoiled so I decided to add that. Leftovers work great for this recipe too!

What Are Egg Muffins?

Egg muffins, sometimes called mini frittatas, are essentially scrambled eggs baked in a muffin tin. Think of them as portable omelets as they are compact, versatile, and incredibly satisfying. You can fill them with your favorite veggies, cheeses, meats, and seasonings. They are so easy to customize and even low carb.

Why You’ll Love This Recipe

• Meal prep friendly – Make a batch on Sunday and enjoy all week.
• Freezer safe – Store extras in the freezer for quick breakfasts on the go.
• Healthy and filling – Packed with protein and customizable for any diet.
• Kid-approved – A great way to sneak in veggies for picky eaters.

Ingredients for Basic Egg Muffins

Here’s what you need to make these ham and cheese egg muffins:

• Eggs
• Frozen peppers and onions (you can also use fresh)
• Deli Ham
• Shredded cheese (cheddar, mozzarella, or your favorite)
• Salt and pepper, to taste
• Non-stick spray or silicone muffin liners

How to Make Egg Muffins (Step-by-Step)

1. Preheat and Prep

Preheat your oven to 350°F Lightly grease a 12 cup muffin tin with cooking spray or line with muffin liners.

2. Whisk the Eggs

In a large bowl, whisk together the eggs. Season with salt and pepper.

3. Saute the Veggies

I like to saute my veggies in a little olive oil until they are soft. You don’t have to do this or can just add them raw if you prefer.

4. Add in all Ingredients

Fold in your veggies, ham and shredded cheese. Feel free to get creative with your ingredients—leftovers work great here!

5. Fill the Muffin Tin

Divide the mixture evenly between the 12 muffin cups.

6. Bake

Bake for 20–25 minutes, or until the centers are set and the tops are slightly golden.

7. Cool and Store

Let the muffins cool for a few minutes in the tin, then transfer to a wire rack. Store in the fridge for up to 5 days or freeze for up to 2 months.

Other Ingredients to Add to Egg Muffins

There are so many ways to make these egg muffins that the possibilities are endless! You could add sausage or bacon instead of ham or even leave the meat out all together to just have a veggie egg muffin.

Egg muffins are a blank canvas. Here are a few delicious combinations to inspire you:

• Ham & Swiss: Diced ham, Swiss cheese, and chives
• Veggie Delight: Zucchini, bell peppers, spinach, and feta
• Southwest: Black beans, corn, jalapeño, cheddar, and cilantro
• Greek Style: Kalamata olives, sun-dried tomatoes, spinach, and feta
• Keto Bacon & Cheese: Crumbled bacon, cheddar, and green onions

How to Store and Reheat

Refrigerator: Store in an airtight container for up to 5 days.
Freezer: Wrap muffins individually and place in a freezer-safe bag or container.
To reheat: Microwave for 30–60 seconds (from fridge) or 90 seconds (from frozen).

These muffins are perfect for busy school mornings, commuting adults, or even a post workout snack.

Are Egg Muffins Healthy?

Yes! Egg muffins are a great source of protein, healthy fats, and depending on the ingredients, vitamins and fiber too. You control the add-ins, so they can be as light or as hearty as you want. Make them vegetarian, low-carb, Whole30, paleo, or high-protein—whatever suits your goals.