Easy & Healthy Caprese Egg Muffins: Your Go-To High-Protein, Low-Carb Breakfast for Meal Prep!
Start your day the delicious and nutritious way with these Caprese Egg Muffins! These flavorful baked egg cups are packed with the fresh taste of cherry tomatoes, fragrant basil, and savory cheese, making them a perfect high-protein, low-carb solution for any meal. Ideal for those following a keto or gluten-free diet, these muffins are not only incredibly easy to make but also fantastic for meal prepping. Whip up a batch, enjoy them throughout the week, or freeze them for quick, on-the-go breakfasts whenever hunger strikes!

Caprese Egg Muffins: The Ultimate Breakfast Solution
Breakfast is often hailed as the most important meal of the day, and for good reason! It kick-starts your metabolism, provides essential energy, and helps you stay focused. However, with our increasingly busy lives, finding healthy and convenient breakfast options can be a real challenge. That’s where these delightful Caprese Egg Muffins come in. They are not just another breakfast recipe; they are a game-changer for anyone seeking a wholesome, quick, and incredibly tasty start to their day.
Imagine waking up on a hectic weekday morning, knowing that a nutritious, warm breakfast is just seconds away. These Caprese Egg Muffins embody convenience, making them an indispensable part of your breakfast routine. They are high in protein, low in carbohydrates, and naturally both keto and gluten-free, catering to a wide range of dietary needs without sacrificing flavor. The classic Italian combination of sweet cherry tomatoes, aromatic fresh basil, and creamy cheese baked into individual egg cups is simply irresistible.
As the weather warms up and local farmers markets begin to burst with fresh produce, this recipe truly shines. Utilizing fresh ingredients like vibrant cherry tomatoes and fragrant basil makes these egg muffins exceptionally delicious. If you’re new to the world of egg muffins, prepare to be amazed! They are incredibly simple to prepare, making them an excellent choice for meal prepping. I often double the batch and freeze half, ensuring I always have a healthy option readily available. A quick minute or two in the microwave, and you’re good to go, transforming frantic mornings into calm, well-fueled beginnings.
For those who love variety, I often rotate between these fantastic Caprese Egg Muffins and other favorites like my Breakfast Egg Muffins, spicy Southwest Taco Egg Muffins, and savory Southwestern Turkey Sausage Egg Cups. Each offers a unique flavor profile while maintaining the same convenience and health benefits.
Why You’ll Absolutely Love These Caprese Egg Muffins:
- Effortlessly Healthy: Packed with protein and fresh vegetables, they keep you full and energized without the heavy carbs.
- Perfect for Meal Prep: Make a large batch on Sunday, and enjoy grab-and-go breakfasts all week long.
- Keto & Gluten-Free Friendly: A naturally compliant option for specific dietary lifestyles, without needing any special ingredients.
- Bursting with Caprese Flavor: The timeless combination of tomatoes, basil, and cheese creates a taste that’s both comforting and gourmet.
- Super Convenient: Quick to reheat and eat, they are ideal for busy mornings or as a healthy snack.
- Freezer Friendly: Easily store extras in the freezer for even longer-lasting convenience.

Ingredients Spotlight: What Makes Caprese Egg Muffins Shine
The beauty of these Caprese Egg Muffins lies in their simple, high-quality ingredients that come together to create a harmonious blend of flavors. Here’s a closer look at what you’ll need and why each component is key:
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Eggs: The Protein Powerhouse
This recipe calls for 12 large eggs, making these egg cups incredibly protein-packed. Eggs are a fantastic source of complete protein, essential for muscle repair and sustained energy. They form the base of our muffins, binding all the delicious components together. Feel free to use organic, free-range, or any eggs you prefer for optimal nutrition and flavor.
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Fresh Basil: The Aromatic Heart of Caprese
Fresh basil is non-negotiable for that authentic Caprese flavor. Its sweet, peppery aroma and vibrant green leaves add a burst of freshness that dried basil simply can’t replicate. Roughly chopped basil leaves infuse the egg muffins with their distinctive, beloved taste. If fresh basil is hard to find, a small amount of dried basil can be substituted, but aim for fresh if possible for the best results.
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Cheese: Creamy Indulgence
A mix of shredded sharp cheddar cheese and mozzarella cheese provides the perfect balance of tang and creamy melt. Cheddar adds a savory depth, while mozzarella contributes to that satisfying gooey texture when baked. You can certainly experiment with other semi-soft cheeses like provolone, Fontina, or even a sprinkle of Parmesan for a saltier kick. Goat cheese or feta would also offer a delightful Mediterranean twist.
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Cherry Tomatoes: Bursts of Sweetness
Sweet and juicy cherry tomatoes are the ideal complement to the basil and cheese. When quartered and baked, they soften slightly and release their sweet juices, adding moisture and vibrant color to each muffin. Their small size makes them perfect for individual egg cups, ensuring every bite gets a taste of sunshine. If cherry tomatoes aren’t available, diced Roma tomatoes or grape tomatoes would also work well.
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Oregano & Seasoning: Flavor Enhancers
A touch of dried oregano adds an earthy, classic Italian herbaceous note that deepens the overall flavor profile of these egg muffins. Combined with simple salt and ground black pepper, these seasonings enhance the natural flavors of the fresh ingredients without overpowering them.

Crafting Your Caprese Egg Muffins: A Simple Guide
Making these delicious Caprese Egg Muffins is surprisingly straightforward. Follow these steps for perfect, fluffy egg cups every time:
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PREHEAT THE OVEN: Begin by preheating your oven to 375 degrees Fahrenheit (190°C). Proper preheating ensures the muffins bake evenly and set correctly, preventing a rubbery texture.
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PREPARE THE MUFFIN TINS: Generously grease your muffin tins. You’ll need enough molds for 16-18 muffins. Make sure to thoroughly oil both the bottoms and sides of each cup. This crucial step prevents sticking and allows for easy removal of your baked egg muffins. Alternatively, you can use paper or silicone muffin liners for even easier cleanup and removal.
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MIX THE EGGS, SALT, PEPPER AND OREGANO: In a medium-sized bowl, crack all 12 eggs. Use a whisk to beat them thoroughly until the yolks and whites are completely combined and slightly frothy. Then, add the salt, black pepper, and oregano to the beaten eggs. Whisk again briefly to ensure all the seasonings are well incorporated. This foundational mix will ensure your Caprese Egg Muffins are perfectly seasoned throughout.
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ADD THE TOMATOES: Gently fold in the quartered cherry tomatoes, roughly chopped fresh basil leaves, and both shredded cheddar and mozzarella cheeses into the egg mixture. Stir just enough to evenly distribute the ingredients. Overmixing can sometimes make egg muffins tough, so a gentle fold is best to keep everything light and airy.
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DIVIDE THE EGG MIXTURE: Carefully divide the colorful egg mixture among the 16 to 18 muffin molds. Aim to fill each cup about 2/3 of the way full. This allows room for the eggs to puff up slightly during baking without overflowing, creating beautifully domed egg muffins.
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BAKE: Transfer the muffin tins to the preheated oven. Bake for approximately 20-25 minutes. Keep an eye on them; the egg muffins are perfectly done when they are set in the middle (no jiggle) and begin to turn a beautiful golden brown around the edges. Avoid overbaking, as this can lead to dry egg muffins.
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COOL AND SERVE: Once baked, remove the muffin tins from the oven. Allow the Caprese Egg Muffins to cool in the tins for a few minutes before attempting to remove them. This cooling period helps them firm up and prevents them from breaking. For easy removal, run a thin knife gently around the edges of each muffin. Serve them warm, or let them cool completely for meal prepping.
Creative Variations: Personalize Your Caprese Egg Muffins
While the classic Caprese combination is undeniably delicious, these egg muffins are incredibly versatile. Don’t hesitate to get creative and customize them to your liking or to use up whatever ingredients you have on hand. Here are some fantastic ways to modify your Caprese Egg Muffins:
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Vegetable Boosters
Beyond the cherry tomatoes, these muffins welcome a variety of other vegetables. Consider adding finely diced bell peppers (any color!), shredded carrots, finely chopped celery, or small florets of broccoli. For a Mediterranean touch, try adding chopped artichoke hearts or sun-dried tomatoes (drained of oil) for an intense flavor. Ensure any larger vegetables are finely chopped so they cook through evenly and integrate well.
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Cheese Adventures
The original recipe uses cheddar and mozzarella, but the cheese world is your oyster! Crumbled goat cheese or salty feta cheese would add a tangy, creamy element. For a nuttier flavor, grate in some gouda or Swiss cheese. A spicy pepper jack cheese could also add a pleasant kick. Feel free to use a blend of your favorite cheeses!
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Leafy Greens & Herbs
Boost the nutritional content and flavor with extra greens. Finely chopped kale or fresh spinach are excellent additions. Simply wilt them slightly before adding to the egg mixture to avoid excess moisture. While fresh basil is key, other fresh herbs like chopped parsley, fresh dill, or a sprinkle of chives can also elevate the flavor profile, especially as a garnish after baking.
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Spice It Up
If you like a bit of heat, consider adding a pinch of crushed red pepper flakes or a tiny dash of cayenne pepper to the egg mixture. For more complex flavor, integrate international spice blends like Middle Eastern za’atar, classic Italian seasoning, or a robust Greek seasoning blend. These spices will add depth and a unique twist to your Caprese Egg Muffins.
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Add Protein Power
For an even heartier breakfast, incorporate cooked and crumbled sausage (turkey or pork), crispy bacon bits, or finely diced cooked ham into the egg mixture. Ensure any meat additions are fully cooked before folding them in.
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A Touch of Acid
After your Caprese Egg Muffins are baked and slightly cooled, a light drizzle of high-quality balsamic glaze can enhance the Caprese flavors beautifully, adding a sweet and tangy finish.

Storing, Freezing, and Reheating Caprese Egg Muffins
One of the biggest advantages of these Caprese Egg Muffins is their meal-prep friendliness. You can make a large batch and enjoy them throughout the week, or even stock your freezer for future busy mornings!
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Refrigeration:
Once your egg muffins have cooled completely, transfer them to an airtight container. Store them in the refrigerator for up to 4 days. They are excellent for grab-and-go breakfasts or quick snacks throughout your week.
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Freezing:
To freeze Caprese Egg Muffins for longer storage, first ensure they are completely cool. Wrap each muffin individually in plastic wrap. This prevents freezer burn and makes it easy to grab just one at a time. Then, place all the individually wrapped muffins into a large freezer-safe ziplock bag or an airtight freezer container. They can be stored in the freezer for up to 2-3 months.
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Reheating:
From the refrigerator: Pop an egg muffin into the microwave for about 30-60 seconds, or until heated through. You can also warm them in a toaster oven at 300°F (150°C) for 5-7 minutes for a crispier exterior.
From the freezer: Remove the plastic wrap from a frozen egg muffin. Reheat it in the microwave for 1-2 minutes, or until thoroughly warm. For best results, especially if you prefer a slightly firmer texture, you can finish reheating them in a toaster oven at 350°F (175°C) for 10-15 minutes after microwaving, or directly in the toaster oven for about 20-25 minutes from frozen (covering loosely with foil to prevent over-browning if needed).
Frequently Asked Questions (FAQ) about Caprese Egg Muffins
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Can I use different types of tomatoes?
Absolutely! While cherry tomatoes offer bursts of sweetness and are perfectly sized, you can use other types. If using larger tomatoes like Roma or regular slicing tomatoes, make sure to dice them into small pieces and consider removing some of the watery seeds to prevent the muffins from becoming too moist.
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Can I make these dairy-free?
Yes, you can! Simply substitute the dairy cheeses with your favorite dairy-free shredded cheese blend. Many brands offer excellent mozzarella and cheddar alternatives that melt well.
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How do I prevent the egg muffins from sticking to the tin?
Generously greasing the muffin tin with cooking spray or butter is key. For extra assurance, you can use silicone muffin liners or paper liners, which make removal incredibly easy. If using metal tins, make sure to let the muffins cool for a few minutes before trying to remove them; this allows them to firm up slightly.
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Are these suitable for a crowd?
Definitely! This recipe yields 16-18 muffins, making it perfect for feeding a family or a small gathering. You can easily double or triple the recipe if you’re hosting a larger brunch or want to significantly boost your meal prep stash.
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Can I add other herbs?
While fresh basil is essential for the Caprese flavor, you can certainly add other herbs for an extra layer of taste. Fresh parsley or chives chopped finely would be wonderful additions. Just be mindful not to overpower the basil.
Other Delicious Breakfast Recipes You’ll Love:
If you’re a fan of these easy and healthy breakfast options, be sure to check out some of my other popular recipes:
MEDITERRANEAN VEGETABLE FRITTATA
MEDITERRANEAN EGG SCRAMBLE
MEDITERRANEAN QUICHE WONTONS
EASY SHAKSHUKA
CHILAQUILES ROJOS
TURKEY SAUSAGE PUFF PASTRY PIZZA
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Caprese Egg Muffins

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Ingredients
- 12 eggs
- 1/2 cup basil leaves, packed
- 1/2 cup cheddar cheese, shredded
- 1/2 cup mozzarella cheese, shredded
- 2 cups cherry tomatoes, quartered {10 ounces}
- 1 teaspoon oregano
- 1/2 teaspoon salt
- 1/8 teaspoon ground black pepper
Instructions
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Preheat the oven to 375 degrees F (190°C).
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Generously grease your muffin tins (enough for 16-18 muffins) and set aside. Ensure both the bottoms and sides of each cup are well-oiled to prevent sticking.
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Place the eggs into a medium-size bowl and beat them thoroughly. Then, add salt, black pepper, and oregano. Whisk to combine all ingredients until well incorporated.
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Gently fold in the chopped cherry tomatoes, roughly chopped fresh basil leaves, and shredded cheese. Stir just enough to evenly distribute the ingredients throughout the egg mixture.
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Divide the egg mixture evenly into 16 to 18 muffin molds, filling each cup about 2/3 of the way full to allow for rising.
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Place the muffin tins in the preheated oven and bake for 20-25 minutes, or until the egg muffins are set in the middle and the edges begin to turn a light golden brown.
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Remove from the oven and let cool in the muffin tin for a few minutes before attempting to remove them.
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Run a thin knife around the edges of each muffin for easy removal from the tin.
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Serve warm, or let cool completely for meal prepping and storage.
Notes
- For this recipe, you can use any semi-soft cheese you like.
- Store these muffins covered, in the fridge, for up to four days. Great for meal planning!
- If you want to freeze these, wrap them in plastic wrap individually and then put them in a large ziplock bag. Remove from the freezer when you are ready to eat them and heat them in the microwave for two minutes or until warm.
Nutrition
Carbohydrates: 1g,
Protein: 6g,
Fat: 5g,
Saturated Fat: 2g,
Polyunsaturated Fat: 1g,
Monounsaturated Fat: 2g,
Trans Fat: 0.01g,
Cholesterol: 129mg,
Sodium: 167mg,
Potassium: 96mg,
Fiber: 0.2g,
Sugar: 1g,
Vitamin A: 370IU,
Vitamin C: 4mg,
Calcium: 67mg,
Iron: 1mg
Nutrition information is automatically calculated, so should only be used as an approximation.