Name: Healthy Ham and Cheese Egg Bites Recipe
Prep time: 10 min
Cook time: 16 min
Total time: 26 min
Cuisine: American
Ingredients: 6 eggs; 3 tablespoons milk; 3/4 cup grated cheddar cheese; 1/4 cup green onion, sliced; 1 cup ham, cut into small cubes; 3/4 cup red bell pepper, chopped; 1/4 cup red onion, chopped; 1/2 tablespoon olive oil; Salt and pepper to taste; Cooking spray for greasing the pan

There’s something incredibly satisfying about these little pockets of flavor — that’s why I’m excited to share this Healthy Ham and Cheese Egg Bites Recipe with you. They’re simple, packed with goodness, and just perfect for busy mornings or a quick snack anytime you need a protein boost.

A group of small, golden-yellow egg muffins stacked close together on a soft brown cloth, each muffin showing a slightly puffy and textured top with bits of green herbs and small orange pieces embedded within. The muffins have a crispy, light brown crust around the base and sides, giving a slightly rough texture. The overall look is warm, soft, and inviting with a rustic touch from the cloth underneath. The background consists of a white marbled texture. Photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Healthy Ham and Cheese Egg Bites Recipe
Top Tip
How to Serve Healthy Ham and Cheese Egg Bites Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Healthy Ham and Cheese Egg Bites Recipe

Why You'll Love This Recipe

I really fell in love with these egg bites because they feel indulgent without any guilt. Plus, they come together quickly and are so adaptable—you can toss in your favorite veggies or swap out the cheese without skipping a beat.

Quick and Easy: Ready in about 25 minutes, they’re perfect for rushed mornings or a mid-day snack.
Nutritious and Filling: Packed with protein and fresh veggies, they keep you satisfied longer.
Customizable: You can easily swap ingredients based on what you have on hand or your dietary preferences.
Great for Meal Prep: Make a batch ahead and enjoy grab-and-go breakfasts all week.

Ingredients & Why They Work

Each ingredient in this Healthy Ham and Cheese Egg Bites Recipe plays a role in balancing taste, texture, and nutrition. I always grab quality cheddar for that melty richness and opt for fresh bell peppers to add a natural sweetness and crunch.

Flat lay of six whole brown eggs with clean shells, a small white ceramic bowl of fresh milk, a small white bowl filled with grated bright orange cheddar cheese, a small white bowl with cubed pink ham, a small white bowl of chopped vibrant red bell pepper, a small white bowl containing chopped purple-red onion, a small white bowl holding thinly sliced green onions, a small white bowl with golden olive oil, and small mounds of coarse salt and freshly ground black pepper, all arranged with perfect symmetry on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Eggs: The star of the show, providing protein and structure to these bites.
Milk: Adds moisture and helps create a creamy, tender texture.
Cheddar Cheese: Offers sharpness and gooeyness that melds beautifully with the eggs.
Ham: Brings a savory, smoky bite and a boost of protein—make sure it’s diced small for even distribution.
Red Bell Pepper: Adds sweetness and a pop of color, plus it softens nicely when sautéed.
Red Onion: Delivers a mild pungency that deepens the flavor profile once cooked.
Green Onion: Sprinkled in for a fresh, bright finish, especially wonderful stirred into the egg mixture.
Olive Oil: Used for sautéing veggies and ham gently without overpowering the flavors.
Salt and Pepper: Essential seasoning to highlight the natural flavors of the ingredients.

📝

Note: You'll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Make It Your Way

I love mixing things up with this Healthy Ham and Cheese Egg Bites Recipe depending on what flavors I’m craving or what’s in my fridge. It’s totally flexible, so don’t be shy about making it your own.

Vegetarian Variation: Skip the ham and double the veggies, or add mushrooms and spinach—I’ve done this many times, and it’s equally delicious.
Cheese Swap: Try pepper jack for a bit of spice or mozzarella for a milder, stretchy bite—I once added feta and loved the tang it brought.
Herbs and Spices: Fresh thyme or smoked paprika can be great additions if you’re feeling fancy.
Low-fat Swap: Use egg whites or reduce cheese to keep it even lighter while still tasty.

Step-by-Step: How I Make Healthy Ham and Cheese Egg Bites Recipe

The image shows six small golden-brown egg muffins placed on a white rectangular plate on a white marbled surface. Each muffin has a rough, puffy top with visible small pieces of green onion inside the muffin and a few green onion rings sprinkled on top. The muffins look soft and slightly crispy around the edges. On the plate, there are three fresh green onion stalks and two orange slices placed beside the muffins. The background is blurred, showing the wooden texture of the surface, with three more muffins in the distance. Photo taken with an iphone --ar 2:3 --v 7

Step 1: Get Your Oven and Pan Ready

Preheat your oven to 350°F (175°C). Don’t skip this, as a fully heated oven ensures your egg bites cook evenly and develop that beautiful golden top. Generously spray a mini muffin pan with cooking spray so the bites pop out easily later.

Step 2: Sauté Ham and Veggies

Warm the olive oil in a skillet over medium heat. Toss in the diced ham, chopped red bell pepper, and red onion. Sauté for about 4-5 minutes until the peppers and onions are just tender—we’re going for softened but still vibrant veggies here. This step brings out flavors and prevents sogginess in the final bites.

Step 3: Whisk Eggs and Milk

In a large bowl or measuring cup, whisk together the eggs and milk until fully combined. If you like your egg bites a bit more dense, try using a fork to blend instead of whisking—it’s a neat trick I picked up that really changes the texture.

Step 4: Combine Everything and Season

Add the grated cheddar cheese and sliced green onions to the egg mixture, then stir in the sautéed ham and veggies. Season with salt and pepper to taste. Give it a final stir to make sure everything’s well incorporated.

Step 5: Bake and Enjoy

Pour the mixture evenly into your prepared mini muffin pan. Bake at 350º F for about 14-16 minutes. You’ll know they’re done when the tops are golden brown and the bites spring back to the touch. Let them cool slightly before removing them from the pan—this helps prevent sticking and keeps their shape intact.

Top Tip

From my many attempts making these egg bites, I’ve picked up a few tricks that make all the difference to your success and flavor.

Season as You Go: Season the ham and veggies while they sauté to build deeper flavor right from the start.
Don’t Overfill Your Muffin Cups: Filling them about ¾ full prevents overflow and helps the bites cook evenly.
Use Fresh Ingredients: Fresh veggies really make a noticeable difference in both texture and taste.
Test Oven Temperature: Every oven’s a bit different, so watch the first batch closely to avoid overcooking and drying out your bites.

How to Serve Healthy Ham and Cheese Egg Bites Recipe

Garnishes

I usually finish mine off with a sprinkle of fresh chives or a little freshly cracked black pepper. Sometimes I’ll add a dollop of avocado or a side of salsa to bring a bit of creaminess and zest to the plate.

Side Dishes

These egg bites pair beautifully with a crisp side salad or some lightly sautéed greens. On chillier mornings, I like to serve them alongside roasted sweet potatoes or fresh fruit for a nicely balanced meal.

Creative Ways to Present

For brunch gatherings, I love putting them on a wooden board with colorful vegetable crudités, small bowls of dips, and fresh herbs—it makes the table look inviting and vibrant. Wrapping a few in parchment paper makes a charming grab-and-go gift, too!

Make Ahead and Storage

Storing Leftovers

Leftover egg bites keep well in an airtight container in the fridge for up to 4 days. I recommend letting them cool completely before storing to avoid condensation that makes them soggy.

Freezing

I freeze these egg bites individually on a baking sheet before transferring them to a freezer bag. They reheat wonderfully and store for up to 2 months. Having these ready in the freezer has saved me countless busy mornings!

Reheating

To reheat, I pop them in the microwave for about 30-45 seconds or until warmed through. You can also reheat in a low oven if you want to keep their texture firm and avoid any rubberiness.

Frequently Asked Questions:

Can I make this recipe dairy-free?

Absolutely! You can swap the cheddar cheese for a dairy-free cheese alternative or simply omit it. Using a plant-based milk like almond or oat milk will keep the texture creamy. I’ve tried this, and it turns out just as tasty.

What’s the best type of ham to use?

Choose a lean, cooked ham that’s not too salty. I prefer using natural or low-sodium ham from the deli to control the saltiness and avoid overpowering the flavors. Dicing it finely helps distribute the flavor evenly.

Can I bake these egg bites without a mini muffin pan?

You can use a regular muffin pan or even a small loaf pan lined with parchment paper. Just adjust the cooking time—larger portions will take longer to set and cook through. I prefer mini muffin pans because they create perfectly portioned bites that cook evenly.

How do I know when the egg bites are done?

Look for a golden brown top and that the egg has completely set with no liquid pooling. A gentle spring back when pressed with your finger is a good sign. Overbaking can make them dry, so keep a close eye near the 14-minute mark.

Final Thoughts

This Healthy Ham and Cheese Egg Bites Recipe has become my go-to for busy mornings and when I want something that feels both wholesome and satisfying. They’re a little kitchen hug wrapped up in a bite-sized bundle, and I’m sure you’ll find they make mornings a bit brighter and easier too. Give them a try—I’d love to hear how you make them your own!