6 Easy Meal Prep Egg Muffins for Stress-Free Mornings

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We’ve all been there: the alarm goes off, the coffee isn’t ready yet, and the thought of standing over a stove to scramble eggs feels like a mountain you can’t climb. I used to grab a granola bar and hope for the best, but I always ended up starving by 10:00 AM. That’s precisely why I fell in love with meal prep egg muffins. These little protein powerhouses are the ultimate solution for busy mornings because they are completely customizable and ready when you are.

Think of this recipe as your morning insurance policy. Whether you are craving a Mediterranean vibe with sun-dried tomatoes or a classic ham and cheese, these breakfast egg muffins deliver every single time. They aren’t just convenient; they are budget-friendly and incredibly satisfying. Today, I’m sharing my favorite Caprese-style base, but I’ll also show you how to mix and match ingredients to keep your breakfast routine feeling fresh and exciting!

A vertical Pinterest graphic titled "Meal Prep Egg Muffins" featuring a stack of golden-brown egg muffins filled with tomatoes and spinach at the top, and a flat-lay view of multiple egg muffin variations, including whole-egg styles and melted cheddar toppings, on a marble surface at the bottom.
Top-down view of several baked egg muffins on a grey stone surface, including variations with whole sunny-side-up style eggs, melted cheddar cheese toppings, and fresh chives sprinkled over white egg bases.

Caprese Breakfast Egg Muffins

Hilary PARKER
The ultimate protein-packed, grab-and-go solution for busy mornings.
Course Breakfast
Cuisine talian-American Fusion
Servings 6 egg muffins
Calories 165 kcal

Ingredients
  

  • 6 large eggs
  • 1 cup sun-dried tomatoes dried or oil-packed
  • 6 ounces fresh mozzarella cheese chopped (or pearl-sized balls)
  • ½ cup fresh basil chopped
  • ½ teaspoon sea salt
  • ½ teaspoon black pepper
  • ¼ teaspoon garlic powder
  • Cooking spray for greasing

Instructions
 

  • Heat it up: Preheat your oven to 350°F and generously spray a 6-cup muffin tin.
  • Soften the tomatoes: If using dried tomatoes, soak in boiling water for 10 minutes, drain, and squeeze dry. Chop roughly.
  • Layer the flavors: Divide tomatoes among the muffin cups.
  • Add the eggs: Crack one egg into each cup directly over the tomatoes.
  • Cheese it: Top each egg with roughly 1 ounce of chopped mozzarella.
  • Season: Sprinkle the salt, pepper, and garlic powder mixture over the cups.
  • Bake: Cook for 10–12 minutes (runny yolks) or 12–15 minutes (firm yolks).
  • Cool and Garnish: Let cool for 10 minutes, remove from the tin, and top with fresh basil.

Notes

  • Fridge: Store in an airtight container for up to 5 days.
  • Freezer: Store for up to 3 months.
  • Reheat: Microwave for 1 minute, or toast in a toaster oven at 350°F for 5–7 minutes.

Nutrition

Calories: 165kcalCarbohydrates: 4gProtein: 11gFat: 12gFiber: 1g
Keyword breakfast egg muffins, egg cups meal prep, healthy egg muffins, high protein egg bites, meal prep egg muffins
Tried this recipe?Let us know how it was!

Why Meal Prep Egg Muffins Work

If you’re wondering why everyone is obsessed with egg cup meal prep, it comes down to pure practicality. First off, the protein content is fantastic; you’re looking at about 7g+ per muffin, which helps keep those mid-morning snack cravings at bay. I also love that they are freezer-friendly for up to three months, making them the king of “future-you” favors.

The best part? They take about one minute to reheat in the microwave. You can literally grab two on your way out the door and have a hot, high-protein egg bite experience at your desk or in the car. Plus, using a muffin tin lets you make several different flavors in a single batch, which is perfect if you’re cooking for a picky family or just someone who likes variety!

The Essentials: Ingredients

For this specific Caprese-inspired version, we are leaning into bold, bright flavors. Here is what you’ll need to gather:

  • 6 large eggs: The foundation of our breakfast egg cups.
  • 1 cup sun-dried tomatoes: You can use dried or oil-packed (just be sure to drain the oil well).
  • 6 ounces fresh mozzarella cheese: Chopped into small bits or use those cute pearl-sized mozzarella balls.
  • ½ cup fresh basil, finely chopped for that hit of freshness at the end.
  • ½ teaspoon sea salt: To bring all the flavors together.
  • ½ teaspoon black pepper: For a little bit of a zippy finish.
  • ¼ teaspoon garlic powder: Just enough to add depth without being overwhelming.
  • Cooking spray: Essential for preventing your muffins from sticking to the pan!

Step-by-Step Instructions

Get ready to transform your morning routine! Here are the steps to create these savory, healthy egg muffins:

1. Prep Your Pan

Preheat your oven to 350°F. Generously spray six cups of a standard muffin tin with cooking spray. I recommend making sure you coat the sides and bottom thoroughly, eggs love to stick, and we want these to pop right out! Set the tin aside while you prep your tomatoes.

2. Prepare the Sun-Dried Tomatoes

If you’re using dried sun-dried tomatoes, place them in a small heat-safe bowl and cover them with boiling water. Let them soak for 10 minutes to reconstitute. Once they’re soft, drain them and squeeze out the excess water with a towel. You want them moist but not dripping! If you’re using oil-packed ones, drain and chop.

3. Build the Base Layer

Divide your chopped sun-dried tomatoes evenly among the six greased muffin cups. This creates a flavorful foundation that gets slightly toasted in the oven. Press them down a bit so they stay put.

4. Add Eggs & Cheese

Carefully crack one egg directly into each muffin cup on top of the tomato layer. You can whisk them beforehand if you prefer a more “omelet” style, but cracking them whole gives a beautiful rustic look. Top each egg with about 1 ounce (2 tablespoons) of the chopped mozzarella.

5. Season to Perfection

In a small bowl, mix your salt, pepper, and garlic powder. Sprinkle this mixture evenly over the six cups. This ensures every bite is balanced and delicious.

6. Bake and Finish

Place the tin in the oven. Bake for 10-12 minutes for soft, slightly runny yolks, or 12-15 minutes for firm yolks. The whites should be set, and the cheese should be bubbly. Let them cool in the tin for 10 minutes (this is key for easy removal!), then run a knife around the edges and lift them out. Sprinkle with fresh basil immediately while they are warm!

A vertical close-up stack of three golden-brown baked egg muffins filled with red sun-dried tomatoes and green spinach, with the top muffin showing a bite taken out to reveal a light, airy interior.

Tips & Variations for Your Egg Muffin Cups

The beauty of egg muffin recipe variations is that you can use whatever you have in your fridge. I personally love the Caprese style, but here are some other ways to switch it up:

  • Classic Ham & Cheddar: Swap tomatoes for diced ham and mozzarella for sharp cheddar.
  • Southwest Style: Use bell peppers, corn, and a dash of chili powder for a savory breakfast muffin.
  • High-Protein Boost: Mix a little cottage cheese into your whisked eggs before pouring. It makes the texture incredibly light and fluffy!
  • Asian-Inspired: Add a drop of sesame oil and some spring onions to the egg mix.

Pro Tip: To prevent a rubbery texture, don’t overbake them! They will continue to firm up slightly as they cool in the tin. If you find your muffins are getting watery, make sure your veggies (like spinach or mushrooms) are sautéed and patted dry before adding them to the eggs.

Top-down view of several baked egg muffins on a grey stone surface, including variations with whole sunny-side-up style eggs, melted cheddar cheese toppings, and fresh chives sprinkled over white egg bases.

Storage & Make-Ahead Guide

  • Fridge: Store in an airtight container for 3-5 days.
  • Freezer: Wrap individual freezer egg muffins in plastic wrap and store in a gallon bag for up to 3 months.
  • Reheating: Use a toaster oven at 350°F for 5-7 minutes to keep the edges crisp, or microwave for 45-60 seconds for a quick fix.

What to Serve With Breakfast Egg Muffins

While these are a complete “grab and go” meal, if you have a little extra time on the weekend, they pair beautifully with other items:

  1. Fresh Fruit Salad: A zippy mix of berries and melon cuts through the richness of the eggs.
  2. Avocado Toast: For some healthy fats, serve two egg muffin cups on top of smashed avocado and sourdough.
  3. Sweet Potato Hash: If you want a heartier brunch, a side of roasted sweet potatoes adds a great textural contrast.
  4. A Simple Green Smoothie: Perfect for getting your greens in alongside your high-protein breakfast.

Frequently Asked Questions

Can I meal prep egg muffins for the whole week?

Absolutely! You can store these in the refrigerator for 3-5 days. I usually make a big batch on Sunday evening, so I don’t have to think about breakfast until Friday.

Why do my egg muffins deflate?

It’s totally normal for them to puff up in the oven and sink a little as they cool. To minimize this, try adding a tablespoon of milk or a dollop of cottage cheese to the mixture, which creates a sturdier structure.

Is it okay to meal prep eggs?

Yes, eggs are a fantastic meal-prep ingredient as long as they are cooked through and stored in an airtight container. They stay fresh and delicious when kept chilled!

Final Thoughts

Making these meal prep egg muffins has honestly changed my morning game. It’s such a relief to know that even on my most chaotic days, I have a healthy, homemade breakfast waiting for me. I hope you have a blast experimenting with different flavor combinations. There really are no wrong answers here!

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