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Egg Muffins with Peppers and Onions

These easy oven baked Egg Muffins with onion, peppers, and cheese are the perfect grab and go breakfast! 

Egg bake muffins in a muffin tin

We love eggs in our house, and generally eat them for breakfast a few days each week. I make baked eggs regularly (like my Baked Eggs with Tomatoes and Feta or Italian Baked Eggs), but I decided to switch it up and use a muffin tin to make these baked egg cups. These baked egg muffins with peppers and onions are quick to prepare and perfect to grab and go.

What’s in Egg Bake Muffins? 

These breakfast egg muffins cups are easy to customize to suit whatever’s in your produce drawer. Here’s what I used for this batch of baked egg cups:

  • Eggs
  • Peppers
  • Onions
  • Milk
  • Shredded cheese
  • Salt and pepper 

How to Make Egg Bake Muffins

  1. Whisk together eggs and milk. 
  2. Stir in peppers, onions, salt, and pepper. 
  3. Divide egg mixture among six greased muffin cups. 
  4. Sprinkle cheese over each breakfast egg muffin cup. 
  5. Bake until the eggs are set. 

How Long to Cook Egg Muffins? 

These easy egg muffins need to bake for approximately 25 to 30 minutes. You’ll know they’re done when the eggs are set.

vegetables in containers

Egg Muffins Variations to Try

I will sometimes use a prepared bag of frozen peppers and onions to make this dish even easier. More often than not I just reach into my refrigerator and pull out whatever veggies I have on hand. We always have snacking peppers, and spinach for smoothies, so those are my two go-to favorites. 

Occasionally I will add in cooked meat, like cubed ham or breakfast sausage.

Can You Freeze Egg Bake Muffins? 

Yes, very easily! Bake the egg muffins in the oven as directed, then let them cool completely before sealing in a freezer bag or freezer-safe container. To reheat, warm in the microwave for about 30 seconds or reheat in the oven.

egg muffin with peppers and onions

Tips for Making Baked Eggs in a Muffin Tin

  • This baked egg cups recipe makes six regular sized egg muffins, but you can easily double this recipe. 
  • Mix and match vegetables and shredded cheeses to use up whatever is in the fridge. 
  • Leftovers will keep in the fridge for up to five days. 

More Easy Breakfast Recipes: 

Egg Bake Muffins with Peppers and Onions

3.85 from 99 votes
Print Pin Rate
Prep Time: 10 minutes
Cook Time: 30 minutes
Total Time: 40 minutes
Servings: 6
Calories: 102kcal
Author: Emily Grace


  • 6 eggs
  • 1/2 cup chopped peppers and onion
  • 1/4 cup milk
  • 2 oz shredded cheese
  • Salt and pepper , to taste


  • Pre-heat oven to 350 degrees F and spray a muffin tin with cooking spray.
  • Whisk together eggs and milk until light and fluffy.
  • Stir in peppers, onions, salt and pepper.
  • Divide egg mixture evenly between six muffin tins (about 1/3 cup each).
  • Sprinkle cheese over each filled cup.
  • Bake until eggs are set, about 25-30 minutes.
  • Allow to cool slightly before serving.


This recipe can easily be doubled.


Calories: 102kcal | Carbohydrates: 2g | Protein: 8g | Fat: 6g | Saturated Fat: 2g | Cholesterol: 172mg | Sodium: 126mg | Potassium: 100mg | Sugar: 1g | Vitamin A: 320IU | Vitamin C: 1mg | Calcium: 87mg | Iron: 0.8mg
Did you make this recipe? Mention @GraceGoodEats or tag #graceandgoodeats!


3.85 from 99 votes (94 ratings without comment)
Recipe Rating


Tuesday 9th of March 2021

Hi, I made these baked eggs and they turned out great. One comment. I find that putting vegetables and cheese into cups first and then pouring in egg mixture allows the ingredients to distribute better. Hope this tips helps. Peggy


Tuesday 5th of May 2020

So excited to try these! Do they freeze well? If not, how long do you think they’d last in the fridge? Thanks!

Maya A.

Sunday 4th of February 2018

OMG!!! I tried this and it is so simple and tasty. My very picky 6 year old cousin loves these too! She doesn't even know that there are veggies in there. Great way to get protein. I make these once a week now. THANK YOU SO MUCH!!!!!!!!!

Kim Cowgar

Tuesday 31st of October 2017

My fave feature is the CrispTray because it promotes proper airflow to help reduce spoilage (and spoiled veggies are gross)

Cami Valenzuela

Tuesday 31st of October 2017

Love how your veggies last longer.. No more waste.

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