Oven Baked Eggs: How To Bake Eggs In A Muffin Tin

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There are several different methods for making oven baked eggs, including egg muffins and cloud eggs. But this time, I’m going to show you how to bake eggs in a muffin tin with the yolks and whites intact. They are an easy meal prep option for when you need a boost of protein, or a delicious addition to your brunch spread.

I first created this type of baked eggs recipe for my first cookbook, The Easy Keto Cookbook, but since then I’ve experimented with about a dozen different ways — so I’m excited to show you what I learned, including all my tips, a time chart, and variations with bacon, veggies, and more.

Can You Bake Eggs?

Yes, you can cook eggs in the oven! In fact, there are several ways to do it. You can make baked boiled eggs right in the shell, create an egg bake (like a breakfast casserole, quiche, or frittata), cook egg muffins (like little omelets in cups) in the oven, or use this recipe for baked eggs in a muffin tin, which keeps the white and yolks separate.

Why You’ll Love This Oven Baked Eggs Recipe

  • One of the easiest baked egg recipes
  • Great way to meal prep a healthy breakfast or snack
  • Just 2 ingredients (plus salt and pepper) for the basic version
  • Endless variations — see ideas below!
  • Minimal cleanup and less dishes to wash
  • Naturally healthy, low carb, and gluten-free
Oven baked eggs on a plate with garnish.

Ingredients You’ll Need

This section explains how to choose the best ingredients for simple baked eggs, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.

It’s super easy to customize your eggs in the oven! You can make a basic version to serve alongside baked bacon and avocado for breakfast, or add meat and/or veggies directly into the cups. I’ll tell you about the combos I used first, then share a formula for endless customizations!

Basic Baked Eggs:

  • Butter – For greasing the muffin tin. You can also use cooking spray (I prefer butter, but sometimes use avocado oil spray for convenience) or coconut oil.
  • Eggs – The cook time for this recipe is based on whole, large eggs. But you can technically do it with any size eggs (cook time will vary), or even just egg whites.
  • Sea Salt & Black Pepper
Ingredients to make basic baked eggs.

Baked Eggs With Bacon:

In addition to the ingredients for plain baked eggs, you’ll also need:

  • Bacon – Regular thickness works better here rather than thick-cut. Also, because you’ll line the muffin cups with bacon, you don’t need to grease them with butter for this version. The same principle can also work with thinly sliced deli meats, such as prosciutto or salami.
  • Cheddar Cheese – Shred your own cheese for best flavor or use shredded for convenience. You could also use a different type of cheese — see the cheese list for ideas.
Ingredients to make bacon baked eggs in a muffin tin.

Baked Eggs With Veggies:

You’ll need the same ingredients as the basic eggs above, plus:

  • Olive oil – For sauteing the veggies. Any other cooking oil, such as avocado oil, also works great.
  • Spinach – We’re using frozen spinach, which makes it extra convenient, but it’s also fine to use fresh. Thaw and drain spinach well.
  • Garlic – Use fresh garlic cloves for best flavor or jarred garlic for convenience.
  • Mushrooms – I like using cremini mushrooms, but you can use any variety.
  • Onions – I used white onions, but you could also use yellow or red onions.
  • Sun-dried tomatoes – Chopped or julienned. Make your own sun-dried tomatoes, or buy them for convenience.
Ingredients to make baked eggs with veggies.
Baked Eggs Formula

Baked Eggs Formula

Want to use different meats or veggies? Use any combination of the below that you like! Here is the formula for making one dozen baked eggs:

  • 12 Eggs – One large egg per egg cup.
  • 2 Cups Fillings – This includes cooked vegetables, cooked meats, or a combination of both. I typically prefer to saute the veggies for flavor, but you can also use leftover steamed or roasted vegetables. Precooked meats, such as as sausage or even shredded chicken, can also be used here. Use about 2.5 to 3 tablespoons of filling per cup, or slightly less if you’re also wrapping the outside in bacon.
  • 1/2 Cup Cheese – This amount equates to about 2 teaspoons for each of the baked eggs, but you can increase that to a tablespoo each if you prefer. Use shredded cheeses, like mozzarella, cheddar, or pepper jack, or crumbled soft cheeses, such as feta or goat cheese.
  • 12 Pieces Sliced Meats – Use one large piece of sliced meat (such as bacon, prosciutto, or salami) per cup, large enough to wrapping all the way around the edges.
  • Salt & Pepper – Use a teaspoon of salt for plain baked eggs, 1/2 teaspoon if you’re using slightly salty fillings (such as sauteed veggies), or 1/4 teaspoon if your add-ins have a lot of salt (such as the bacon and cheddar combo).
  • Something For Greasing – To prevent the eggs from sticking to your muffin tin or ramekins, grease with butter or oil of your choice. You can skip this step if you’re wrapping the edges in bacon or other fatty meats.

How To Bake Eggs In A Muffin Tin

This section shows how to make baked eggs in a muffin tin, with step-by-step photos and details about the technique. For full instructions, see the recipe card below.

  1. Prep. Preheat the oven. Generously grease bottom and sides of muffin tin (unless you’ll be including bacon!).
  2. Cook wrappers (if any). If you want your baked eggs wrapped in bacon (or other meat), wrap the pieces around the edges of the muffin tin and bake until cooked, but not crispy.
  3. Cook fillings (if any). Saute the vegetables (or any meats you want to use for filling) in a skillet. For my veggie combo, I sauted the garlic irst, then onions and mushrooms, and finally the sun-dried tomatoes and spinach, all in the same skillet. Divide the veggies among the muffin cups.
Bacon in muffin cups for baking eggs.
Cooked vegetables in muffin tin.
  1. Crack. Crack an egg into each muffin tin well. Season with salt and pepper.
  2. Bake. Cook eggs until the yolk reaches your desired doneness. (See recommended time chart below.)
Raw eggs in muffin tin.
Oven baked eggs in a muffin tin.

How Long To Bake Eggs?

You can customize the cook time, depending on how you like the yolks. Use the following time chart for perfect baked eggs.

Desired Doneness Minutes At 350 Degrees F
Runny yolks 10-13 minutes
Medium yolks 12-16 minutes
Firm yolks 15-20 minutes

Can You Make Baked Eggs In A Ramekin?

Yes, if you would rather not cook the eggs in a muffin tin, you can use ramekins instead (these are the perfect size). If you’re making a larger quantity in ramekins, it can be convenient to place them into a baking dish for easy transfer to and from the oven.

Baked eggs recipe with bacon.
Baked eggs recipe with vegetables.

Variation Combos

There are so many variations we can make with baked egg cups! Here are a few ideas:

  • Denver Omelet – Follow directions for baked eggs with veggies, but use a combination of green bell pepper, onion, ham, and cheese.
  • Tex Mex – After the egg cups are done cooking, top with fresh tomato salsa and guacamole. You can also include some barbacoa, sauteed bell peppers, and Mexican bled or Cotija cheese in the filling.
  • Ham and Cheese – Add diced ham and shredded swiss or gruyere cheese into the muffin cups before the eggs.
  • Caramelized Onions – After you caramelize onions, place a teaspoon or two into each muffin cup before cracking an egg over it.
  • Broccoli CheeseSaute broccoli (or you can roast the broccoli instead), place in the muffin tin, top with cheddar, and add the eggs.
  • Greek – Sauteed bell peppers and red onions, sliced olives, seeded diced tomatoes, and crumbled feta. Serve with fresh basil.
  • Garlic Parmesan – Sauteed minced garlic, Italian seasoning (or fresh herbs like pasley and chives), and shredded parmesan cheese. This version also pairs well with virtually any cooked veggies.

Storage Instructions

  • Store: Keep these easy eggs in fridge for 3-4 days.
  • Meal prep: Make these baked egg bites ahead and reheat right before serving.
  • Reheat: Reheat eggs in the microwave for about 20-30 seconds, or for better results, in a 350 degrees F oven. The yolks can easily become overcooked when reheating, so watch closely and stop heating as soon as they are just warm. (I’ve done this with great success — I made 5 dozen (!) baked eggs when testing this recipe, so trust me when I say had experience reheating them!)
  • Freeze: The texture can change a little, but you can store baked eggs in the freezer for 2-3 months. Reheat right from frozen.
Cooked eggs in a muffin tin, transferred to a plate.

What To Serve With Baked Eggs

Baked egg recipes like this one can easily be a meal on their own, but for a full breakfast or brunch spread, here are some serving ideas:

More Healthy Egg Recipes

If you like these easy baked eggs, try out some of these other easy healthy egg recipes:

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Tap on the times in the instructions below to start a kitchen timer while you cook.

Basic Baked Eggs:

  1. Preheat the oven to 350 degrees F (176 degrees C).

  2. Generously grease the bottom and sides of the cups of a muffin tin with butter, coconut oil, or avocado oil spray. (You can also use 4-ounce ramekins instead, or silicone muffin cups in a muffin pan instead.)

  3. Crack an egg into each muffin cup. Season with salt and pepper.

  4. Bake eggs in the oven for 10-13 minutes for runny yolks, 12-16 minutes for semi-firm yolks, or 15-20 minutes for firm yolks.

Baked Eggs With Veggies:

  1. Preheat the oven to 350 degrees F (176 degrees C).

  2. Place the thawed spinach into a kitchen towel and squeeze well over the sink, getting rid of as much liquid as possible. Set aside.

  3. Generously grease the bottom and sides of the cups of a muffin tin with butter or coconut oil. (You can also use 4-ounce ramekins instead, or silicone muffin cups in a muffin pan instead.)

  4. In a large skillet, heat the oil over medium-high heat. Add the minced garlic and sauté for about 1 minute, until fragrant.

  5. Add the mushrooms and onions. Cook for 7-10 minutes, until the mushrooms and onions are soft and starting to brown.

  6. Add the spinach and sun-dried tomatoes. Season with the sea salt and black pepper. Sauté for 5 minutes.

  7. Divide the spinach mixture evenly among the muffin cups. Crack an egg into each muffin cup. Season lightly with salt and pepper (you don’t need much salt because the veggie mixture is salted).

  8. Bake eggs in the oven for 10-13 minutes for runny yolks, 12-16 minutes for semi-firm yolks, or 15-20 minutes for firm yolks.

  9. Allow the baked eggs to cool in the pan for a few minutes before removing.

Baked Eggs With Bacon:

  1. Preheat the oven to 350 degrees F (176 degrees C).

  2. Line the sides of each cup of a muffin tin with a slice of bacon, wrapping it around. (You don’t need to grease the muffin cups, since the bacon will render fat.

  3. Place the muffin tin with the bacon in the oven for 10 minutes. Remove from the oven and pat excess grease from the cups with paper towels (you can also remove the bacon and pour off the grease to save it, but this is more work to remove and then put back the bacon pieces). If any of the bacon pieces curled into the center, spread them out toward the perimeter of the muffin cups, to make room for the eggs.

  4. Crack an egg into each muffin cup. Season with sea salt and black pepper. Top with shredded cheddar cheese.

  5. Bake eggs in the oven for 10-13 minutes for runny yolks, 12-16 minutes for semi-firm yolks, or 15-20 minutes for firm yolks.

  6. Allow the baked eggs to cool in the pan for a few minutes before removing.

Recipe Notes

Serving size: 1 baked egg

Nutrition info is for the basic baked eggs recipe, without add-ins.

Nutrition Facts

Amount per serving. Serving size in recipe notes above.

Calories 76

Fat 5.2g

Protein 6.3g

Total Carbs 0.4g

Net Carbs 0.3g

Fiber 0.1g

Sugar 0.2g

Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.

© Copyright Maya Krampf for Wholesome Yum. Please DO NOT SCREENSHOT OR COPY/PASTE recipes to social media or websites. We’d LOVE for you to share a link with photo instead. 🙂

How to bake eggs in a muffin tin: pin graphic.

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