Name: Ham and Cheese Egg Cups
Prep time: 10 min
Cook time: 20 min
Total time: 30 min
Ingredients: 8 large eggs; 0.5 cup milk; 1 cup diced cooked ham; 1 cup shredded cheddar cheese; 0.25 cup chopped onion; 0.25 cup diced bell pepper; 2 tbsp chopped parsley; 0.5 tsp salt; 0.25 tsp black pepper

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Busy mornings don’t have to mean skipping breakfast or grabbing something unhealthy on the go. These Ham and Cheese Egg Cups are the perfect solution for anyone looking for a healthy breakfast muffin that’s easy to prepare, packed with protein, and ideal for meal prep.

If you’ve been searching for a make ahead egg muffin recipe that’s low in carbs, high in flavor, and freezer-friendly, this is it. These savory egg cups combine fluffy baked eggs, smoky ham, and melty cheese into perfectly portioned muffins that reheat beautifully. Whether you’re prepping for the week, feeding a family, or simply trying to eat healthier, this recipe will quickly become a staple.

Why You’ll Love These Ham and Cheese Egg Cups

There are countless breakfast recipes out there, but these healthy breakfast muffins stand out for several reasons:

Quick to prepare – Minimal prep and simple ingredients.
High in protein – Eggs and ham provide long-lasting energy.
Low carb & gluten-free – Perfect for keto or low-carb lifestyles.
Meal prep friendly – Store in the fridge or freezer.
Kid-friendly – Simple, familiar flavors everyone loves.

Unlike sugary breakfast pastries or carb-heavy options, these egg cups help stabilize your energy levels throughout the morning.

What Are Egg Cups?

Egg cups are essentially mini frittatas baked in a muffin tin. Inspired by classic brunch dishes, they deliver the flavor of a full omelet in a compact, portable form. While traditional omelets require stovetop attention, egg cups bake hands-free in the oven, making them ideal for batch cooking.

Think of them as savory breakfast muffins—without the flour.

Ingredients

Here’s everything you need to make these delicious ham and cheese egg cups:

8 large eggs
½ cup milk (or unsweetened almond milk)
1 cup diced cooked ham
1 cup shredded cheddar cheese
¼ cup finely chopped onion
¼ cup diced bell pepper
2 tablespoons chopped fresh parsley
½ teaspoon salt
¼ teaspoon black pepper
Cooking spray or olive oil for greasing

These simple ingredients come together to create a fluffy, flavorful breakfast option that feels indulgent while staying healthy.

Instructions

Preheat your oven to 350°F (175°C). Lightly grease a 12-cup muffin tin with cooking spray or olive oil.
In a large mixing bowl, whisk together the eggs and milk until fully combined and slightly frothy.
Stir in the diced ham, shredded cheese, onion, bell pepper, parsley, salt, and pepper. Mix well.
Carefully pour the egg mixture evenly into the prepared muffin cups, filling each about ¾ full.
Bake for 18–22 minutes, or until the centers are set and the tops are lightly golden.
Remove from the oven and let cool for 5 minutes before gently running a knife around the edges to release each egg cup.
Serve warm or allow to cool completely before storing for meal prep.

Tips for Perfect Egg Muffins

1. Don’t Overfill

Eggs expand as they cook. Filling the muffin cups about three-quarters full prevents overflow.

2. Use Silicone Liners

If sticking is a concern, silicone muffin liners work beautifully.

3. Avoid Overbaking

Overcooked eggs can become rubbery. Remove them once the centers are just set.

4. Chop Ingredients Finely

Smaller pieces distribute more evenly and prevent heavy fillings from sinking.

Make-Ahead & Storage Guide

One of the biggest advantages of these ham and cheese egg cups is how well they store.

Refrigerator:

Store in an airtight container for up to 4 days.

Freezer:

Wrap individually and freeze for up to 2 months.

Reheating:

Microwave: 30–60 seconds
Oven: 8–10 minutes at 325°F
Air fryer: 3–4 minutes

They reheat beautifully without losing texture, making them ideal for busy weekdays.

Nutritional Benefits

These healthy breakfast muffins are:

High in protein – Keeps you full longer
Low in carbohydrates – Great for keto or low-carb diets
Gluten-free – Naturally flourless
Balanced in fats and nutrients

Eggs are rich in essential nutrients like vitamin B12, choline, and selenium, making this recipe both satisfying and nourishing.

Flavor Variations

One of the best things about make ahead egg muffins is how customizable they are.

Veggie Lovers

Swap ham for spinach, mushrooms, and zucchini.

Spicy Kick

Add diced jalapeños or a pinch of red pepper flakes.

Mediterranean Style

Use feta cheese, olives, and sun-dried tomatoes.

Breakfast Sausage

Replace ham with cooked sausage crumbles.

Serving Suggestions

These ham and cheese egg cups pair perfectly with:

Fresh fruit salad
Avocado slices
Whole-grain toast
Greek yogurt
Smoothies

They’re also great for brunch spreads, baby showers, or picnic baskets.

Why This Is the Ultimate Meal Prep Breakfast Idea

Meal prepping can feel overwhelming, but this recipe simplifies everything. In under 30 minutes, you can prepare a protein-packed breakfast for the entire week. No morning stress. No skipped meals.

If you’re aiming to eat healthier, manage weight, or simply save time, these low carb breakfast muffins deliver convenience without sacrificing flavor.

Common Questions

Can I make these dairy-free?

Yes! Use unsweetened almond milk and dairy-free cheese.

Can I use egg whites only?

Absolutely. Replace whole eggs with 2 cups of liquid egg whites.

Why did my egg cups deflate?

They naturally puff up while baking and slightly deflate as they cool—this is completely normal.

Final Thoughts

These Ham and Cheese Egg Cups are everything a healthy breakfast should be: easy, nutritious, flavorful, and convenient. Whether you’re meal prepping for a busy workweek or preparing a quick family breakfast, these savory egg muffins will simplify your mornings while keeping you satisfied.

Make a batch today and experience the difference a well-prepared breakfast can make in your daily routine.