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Two Stacks of Breakfast Egg Muffins of Various Flavors with a Ham and Cheese Muffin in the Front

Egg Muffins – 9 Ways

Need a healthy make-ahead breakfast that can easily be taken to work or school? With just 5 minutes of prep time, these Easy Breakfast Egg Muffins are the ticket. Choose from 9 delicious flavor variations! Naturally gluten-free, grain-free, dairy-free, keto and Whole30 with Paleo options.

Course Breakfast
Cuisine American
Keyword breakfast egg muffins, easy breakfast ideas, keto breakfast muffins
Prep Time 7 minutes
Cook Time 15 minutes
Total Time 22 minutes
Servings 12
Calories 53 kcal
Author Kelly

Ingredients

Base Ingredients

  • 10 large eggs
  • 1 - 1 1/2 teaspoons sea salt, or to taste
  • 1/4 - 1/2 teaspoon black pepper, or to taste

Broccoli and Cheese

  • 1/2 teaspoon dried thyme
  • 1/2 teaspoon garlic powder
  • 1 1/2 cups broccoli, steamed and chopped (or frozen and thawed)
  • 2/3 cup grated cheddar cheese, plus more for topping

Buffalo Chicken

  • 1/2 teaspoon garlic powder
  • 1/3 cup Buffalo Sauce (I used Frank's)
  • 1/3 cup chopped green onions
  • 1 cup chopped cooked (or rotisserie) chicken

Ham and Cheese

  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 1/2 teaspoon dried mustard or Dijon Mustard (optional)
  • 2/3 cup grated cheddar cheese plus more for topping
  • 3/4 cup chopped cooked or deli ham

Kimchi

  • 1/2 teaspoon toasted sesame oil
  • 1/3 cup finely chopped kimchi
  • 1/4 cup diced red peppers
  • 1/3 cup crumbled cooked bacon (optional)

Jalapeño Popper

  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 3-4 jalapeño peppers de-seeded and chopped, plus round slices for topping (if desired)
  • 1/3 cup softened cream cheese
  • 1/2 cup grated cheddar cheese
  • 1/3 cup cooked crumbled bacon

Bacon, Mushrooms and Spinach

  • 1 cup chopped spinach
  • 1/2 cup chopped mushrooms (white button or cremini)
  • 3 strips cooked and crumbled bacon , use Whole30 compliant bacon as needed

Spinach and Cheese

  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon dried basil
  • 2 cups chopped spinach
  • 1 1/2 cups grated Parmesan cheese, plus more for topping

Sun-Dried Tomato, Parmesan and Spinach

  • 1/3 - 1/2 cup sun dried tomatoes soaked in very warm water until tender and chopped (discard soaking water)
  • 3/4 cup chopped spinach
  • 1/4 cup loosely packed chopped fresh basil
  • 1 cup grated Parmesan cheese plus more for topping

Tomato and Spinach

  • 1/2 teaspoon garlic powder
  • 3/4 teaspoon Italian seasoning
  • 1 cup diced ripe tomatoes
  • 1 cup chopped spinach
  • Optional: Feel free to add 3/4 cup grated Parmesan if not Paleo / Whole30 or Dairy Free

Instructions

Base Recipe

  1. Preheat oven to 400 F. Line a 12 count muffin pan with silicone liners or coat with non-stick cooking spray. Set aside.

    9 Breakfast Egg Muffin Cups are the perfect easy make-ahead breakfast for on the go. Best of all, they are packed with protein and so convenient for busy mornings, weekend or holiday brunch! Broccoli and Cheddar Cheese, Buffalo Chicken, Ham and Cheddar Cheese, Jalapeno Popper, Kimchi, Mushroom, Pepper and Spinach, Sun-Dried Tomato and Spinach, Tomato, Basil and Parmesan
  2. In a large 4 cup measuring cup or mixing bowl, crack in eggs and whisk together with salt and black pepper.

    (SEE BELOW TO ADJUST FOR DIFFERENT FLAVORS OR LEAVE AS IS FOR PLAIN)

    Divide evenly into muffin tins filling each about 2/3 full. Bake in preheated oven for 12-15 minutes, or until set.

    9 Breakfast Egg Muffin Cups are the perfect easy make-ahead breakfast for on the go. Best of all, they are packed with protein and so convenient for busy mornings, weekend or holiday brunch! Broccoli and Cheddar Cheese, Buffalo Chicken, Ham and Cheddar Cheese, Jalapeno Popper, Kimchi, Mushroom, Pepper and Spinach, Sun-Dried Tomato and Spinach, Tomato, Basil and Parmesan
  3. Bake in preheated oven for 12-15 minutes, or until set.

    9 Breakfast Egg Muffin Cups are the perfect easy make-ahead breakfast for on the go. Best of all, they are packed with protein and so convenient for busy mornings, weekend or holiday brunch! Broccoli and Cheddar Cheese, Buffalo Chicken, Ham and Cheddar Cheese, Jalapeno Popper, Kimchi, Mushroom, Pepper and Spinach, Sun-Dried Tomato and Spinach, Tomato, Basil and Parmesan

Broccoli and Cheddar

  1. Whisk in garlic powder and thyme until combined. Stir in broccoli and cheddar. Divide evenly into muffin tins filling each about 2/3 full.

    Sprinkle with more cheddar if desired. Bake in preheated oven for 12-15 minutes, or until set.

    A Close-Up Shot of a Broccoli and Cheese Egg Muffin with a Gray Background

Buffalo Chicken

  1. Whisk in garlic powder and buffalo sauce until combined. Stir in green onions. Divide evenly into muffin cups filling each about 2/3 full.

    Use a spoon to evenly distribute chicken into muffin cups (about 2-3 tablespoons each). Bake in preheated oven for 12-16 minutes, or until set. Serve with a drizzle of buffalo sauce if desired.

    A Buffalo Chicken Egg Muffin on a Countertop Beside Some Shredded Chicken and a Dish of Buffalo Sauce

Ham and Cheddar

  1. Whisk in garlic powder and onion powder until combined. Stir in ham and cheddar cheese. Divide evenly into muffin cups filling each about 2/3 full.

    Top with more ham and cheese if desired. Bake in preheated oven for 12-15 minutes, or until set.

    A Ham and Cheese Egg Muffin on a Gray Surface Beside a Small Dish of Shredded Cheddar Cheese and Ham

Kimchi

  1. Whisk in sesame oil until combined. Stir in kimchi, cheese, and bacon (if using). Divide evenly into muffin cups filling each about 2/3 full.

    Top with more chopped kimchi & bacon if desired. Bake in preheated oven for 12-15 minutes, or until set.

    A Kimchi Egg Muffin Cup Sitting on a Gray Surface with Two Small Dishes Next to it

Jalapeño Popper

  1. Whisk in garlic powder, onion powder, and cream cheese until combined. Stir in cheddar cheese, chopped jalapeño and bacon. Divide evenly into muffin cups filling each about 2/3 full.

    Place 1 round jalapeño slice on top in each muffin cup, if desired. Bake in preheated oven for 12-17 minutes, or until set.

    A Jalapeno Popper Egg Muffin on a Countertop Shot From Above

Mushroom, Green Pepper and Spinach

  1. Whisk in Italian seasoning until combined. Stir in mushrooms, peppers, and spinach (Add sausage if using). Divide evenly into muffin cups filling each about 2/3 full.

    Bake in preheated oven for 12-16 minutes, or until set.

    Mushroom, Pepper and Spinach Breakfast Egg Muffin Cups are the perfect easy make-ahead breakfast for on the go. Best of all, they are packed with protein and so convenient for busy mornings, weekend or holiday brunch! Broccoli and Cheddar Cheese, Buffalo Chicken, Ham and Cheddar Cheese, Jalapeno Popper, Kimchi, Mushroom, Pepper and Spinach, Sun-Dried Tomato and Spinach, Tomato, Basil and Parmesan

Spinach and Cheese

  1. Whisk in garlic powder and basil until combined. Stir in spinach and cheese. Divide evenly into muffin cups filling each about 2/3 full.

    Sprinkle with more cheese if desired. Bake in preheated oven for 12-15 minutes, or until set.

    Spinach and Cheese Egg Muffins are quick, simple and make a perfect grab and go breakfast for busy mornings. Best of all, this recipe is easy to customize and the egg cups are low in carbs, keto friendly and packed with protein.

Sun-Dried Tomato, Parmesan and Spinach

  1. Stir in sun-dried tomatoes, spinach, basil, and cheese. Divide evenly into muffin cups filling each about 2/3 full.

    Sprinkle with more cheese if desired. Bake in preheated oven for 12-16 minutes, or until set.

    A Sun-Dried Tomato and Spinach Egg Cup on a Countertop Beside a Spinach Leaf

Tomato and Spinach

  1. Whisk in garlic powder and Italian seasonings until combined. Stir in tomatoes and spinach. You can add cheese here if using. Divide evenly into muffin cups filling each about 2/3 full.

    Sprinkle with more cheese if desired. Bake in preheated oven for 12-16 minutes, or until set.

    A Tomato, Parmesan and Spinach Breakfast Muffin on a Counter with Fresh Basil and Tomato

Recipe Video

Recipe Notes

How to Store and Reheat Leftovers

To store: Individual egg muffins keep best when tightly covered in plastic wrap and refrigerated, but you can store them in an airtight bag or container too. Enjoy them within 4 days.

How to reheat: 

  • Microwave: Warm up individual egg muffins in the microwave for about 30-40 seconds. 
  • Oven: Reheat baked egg cups in the oven or toaster oven at 350°F for about 8-10 minutes, or until warm.
  • Air Fryer: You can also reheat them in the Air Fryer or oven at 375°F for 3- 5 minutes or until warm.

How to freeze

Freeze breakfast egg muffins in a large freezer bag or airtight container for up to 3 months. Individually-stored egg muffins should be wrapped in a layer of plastic wrap and a layer of aluminum foil to prevent freezer burn. Thaw them overnight in the fridge before warming them up or add a little extra reheating time and enjoy!

Nutrition Facts
Egg Muffins – 9 Ways
Amount Per Serving (1 muffin (base recipe))
Calories 53 Calories from Fat 27
% Daily Value*
Fat 3g5%
Carbohydrates 1g0%
Sugar 1g1%
Protein 5g10%
* Nutrition facts are provided as a courtesy using the WPRM recipe calculator. It is best to make your own calculations to ensure accuracy. We expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website. Percent Daily Values are based on a 2000 calorie diet.