How to Meal Prep Eggs (Homemade Egg Bites)

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Whether you call them meal prep eggs, baked eggs, egg bites, or egg muffins; these simple make-ahead scrambled eggs are perfect for weekly meal prep and can save a lot of time on busy mornings.

Breakfast is so important, but it can often be overlooked when you’re busy trying to take care of the rest of the people in your family and make sure they are dressed/fed/clean and ready for the day. 

As a busy mom of four, I often find myself skipping breakfast or meals in general. When life gets busy, my needs tend to fall by the wayside.

Want more healthy meal prep recipes? Make sure to check out our full list of make-ahead breakfasts, too.

An instant pot egg bit on a white and green plate next to a red striped towel.
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❤️Why You’ll Love This Recipe

Meal prep breakfast is the easiest way to avoid convenience foods. These eggs are low-carb and perfect for busy people looking for a better breakfast. 

This recipe is for you if: 

  • If you often find yourself skipping breakfast
  • You want a quick and healthy breakfast option ready for the entire week
  • You like options – this recipe is versatile! You can add in bacon, sausage, cheese, or your favorite veggies! You can also use it as an excuse to use up whatever is sitting in your fridge. 
  • You want to stock your freezer. These egg bites are completely freezer-friendly and are a great way to prepare for an upcoming busy season life. Also check out this post:   14 crockpot freezer meals in 1 day
  • You want an easy way to enjoy a delicious meal quickly. Making a big batch of these eggs allows you to enjoy a quick breakfast with fresh ingredients every day of the week.

You can prep and bake these egg muffins while doing other things in the kitchen – or around the house. Then you’ll have no excuse to skip breakfast!

Sometimes, I will prep these make-ahead scrambled eggs for the freezer alongside other favorite breakfast recipes like a batch of Blueberry Baked Oatmeal, Freezer-Friendly Breakfast Burritos, and breakfast Ham and Egg Breakfast Sandwiches.

Have an instant pot? Try my recipe for Instant Pot Egg Bites!

A muffin pan filled with ingredients for meal prep eggs over a freezer bag filled with frozen egg bites.


Fresh Eggs: 12 large eggs are used in this recipe. Using a different-sized egg will yield different quantities. 

Sausage: Turkey breakfast sausage links cut into chunks.

Green Onions: This adds a great pop of freshness!

Cheese: Cheddar cheese is my go-to for oven-baked eggs and scrambled eggs!

Scroll to the bottom for the complete list of ingredient measurements and printable recipe card.

📖 Ingredient Swaps

Egg Whites: If you prefer egg whites, they can be substituted for whole eggs. However, you will need to add more egg whites (a total of approximately 16) to make up for the lack of egg yolks.

Cheese: Use your favorite cheese! Mexican blend and pepper jack are great options! The cheese can also be omitted altogether. 

Meat: If you want to make vegetarian eggs, feel free to omit the sausage. The turkey sausage can be swapped out for bacon, pork sausage links, or any other kind you like. Just make sure to cut it into smaller pieces. 

Favorite Vegetables: This is where the recipe gets very versatile. You can use any fresh vegetables you have on hand (cut into small bite-sized pieces), here are some ideas: 

  • Fresh spinach
  • Bell Peppers
  • Sweet Potatoes (precooked sweet potato hash would be perfect)
  • Tomatoes
  • Red Onions
  • Fresh Herbs

🔪Step-by-Step Instructions

A muffin tin with a cracked egg inside each slot.
Step 1: Grease the muffin pan. Crack an egg into each muffin pan slot and whisk with a fork.
A muffin tin filled with raw eggs, turkey sausage, and sliced green onions.
Step 2: Add chopped turkey sausage, sliced green onions, salt, and pepper to each egg.
Baked meal prep eggs inside a muffin pan.
Step 3: Bake in a 350ºF oven for 18 minutes, until set and no longer jiggly.
Meal prep eggs topped with shredded cheddar cheese.
Step 4: Top each egg bite with shredded cheddar cheese.
Egg bites topped with melted cheddar cheese.
Step 5: Broil egg bites just until melted, approximately 30 seconds.
Baked egg muffins spread out on a piece of foil.
Step 6: Flash freeze. Arrange egg bites 1 inch apart on a cookie sheet. Freeze for 1-2 hours. (optional)
Meal prep eggs frozen and in a freezer friendly bag.
Step 7: Place frozen egg bites in a freezer-friendly bag. Store in the freezer until ready to eat. Reheat individual egg muffins in the microwave for 1 1/2 – 2 minutes 50% power.

👩🏻‍🍳Expert Cooking Tips

Adding Vegetables

Some vegetables are more tender than others. If the vegetable you are using is on the crunchier side, then you will want to saute them in a tablespoon of olive oil before mixing them in with the eggs. 

Balancing out the meal

If you want to pair these egg muffin cups with something else to make it a more complete meal, you can try serving it on an English muffin or with a side of fresh fruit. A green smoothie is also a great option, but a bit more time-consuming.

Keeping it Fresh

Plan on freezing any egg bites you won’t eat in 3 days. The rest can be stored in the refrigerator in an airtight container.

Reheating meal prepped eggs

These egg bites can be warmed in several different ways. My go-to is the microwave. 30 seconds for refrigerated egg bites and 60-90 seconds and 50% power for frozen egg bites.

Egg bites can also be reheated in the oven, toaster oven, or air fryer. The best way to know the eggs are done and not still frozen in the middle is with a  probe thermometer. The eggs should reach an internal temperature of 160ºF.

​Easy Clean-Up

Eggs tend to want to stick to the muffin pan. For best results, either spray each muffin slot with cooking spray or line them with silicone muffin liners.

💭Recipe FAQs

Is it OK to meal prep eggs?

Yes. Meal prep eggs are a great way to ensure you eat breakfast each day.

How long can you meal prep eggs for in the fridge?

Refrigerated cooked eggs will stay fresh in the fridge for 3-4 days. For best results, make sure your fridge is set to 40ºF or lower.

Can you microwave eggs for meal prep?

You can, but I would only recommend microwaving one egg at a time. Simply whisk up one egg with a teaspoon of milk and salt and pepper to taste. Pour in a ceramic mug or cook and cook until set 45-60 seconds.

How long are cooked eggs good for?

Cooked eggs stay fresh in the fridge for 3-4 days and fresh in the freezer for one year with a freezer temp set to 0ºF or lower.

🥣 More Breakfast Recipes…

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If you tried this Meal Prep Eggs Recipe or any other recipe on my website, I would love it if you could leave me a 🌟 star ratingand let me know how you liked it in the 📝 comments below. ❤️

Freezer Friendly Ham and Egg Breakfast Sandwiches. Make ahead meals. Freezer Cooking. Once A Month Cooking. Freezer Friendly Breakfast. Recipe from

Meal Prep Eggs Recipe

Aileen Clark
Make Ahead Scrambled Eggs are perfect for meal-prep. This make-ahead breakfast freezer meal is perfect for busy mornings and can be customized to your tastes.
4.34 from 30 votes
Prep Time 10 minutes
Cook Time 18 minutes
Total Time 28 minutes
Cuisine American
Servings 12
Calories 141 kcal


  • 12 eggs
  • 4 turkey sausage links sliced
  • 2 green onions sliced
  • 1/2 cup cheese
  • salt and pepper


  • Preheat your oven to 350 degrees.
  • Grease a muffin pan and crack one egg into each opening.
  • Lightly whisk with a fork and place sausage and green onions in the center of each egg. Season with salt and pepper.
  • Bake 18 minutes, or until eggs are set.
  • Set oven to broil.
  • Sprinkle each baked egg with shredded cheese.
  • Return to oven for 30 seconds, just until cheese is melted.
  • Let cool.
  • Place the make ahead scrambled eggs onto a lined cookie sheet in freezer.
  • Once frozen, slide the make ahead scrambled eggs into a gallon sized freezer bag.
  • Label and freeze up to 1 month.
  • To reheat: cook in the microwave for 2 minutes.


Serving: 1egg muffinCalories: 141kcalCarbohydrates: 1gProtein: 14gFat: 9gSaturated Fat: 3gPolyunsaturated Fat: 2gMonounsaturated Fat: 3gTrans Fat: 0.1gCholesterol: 197mgSodium: 317mgPotassium: 169mgFiber: 0.1gSugar: 0.2gVitamin A: 333IUVitamin C: 1mgCalcium: 67mgIron: 1mg
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  1. I am trying your recipe for the first time today my fiancé and our friend are both big eaters and I am not a morning person let’s see how it goes

  2. Pingback: Freezer Cooking for Baby - Aileen Cooks