Breakfast Egg Muffins – 9 Ways

These easy Egg Muffins are a healthy make ahead breakfast for on the go that you can make 9 different ways. Just 5 minutes of prep time and so convenient for busy mornings, weekend or holiday brunch. Low carb, keto-friendly and packed with protein.

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Updated June 2019

EGG MUFFINS ARE A QUICK AND HEALTHY BREAKFAST

Eggs of any kind are a favorite at our house. They are incredibly nutritious, low in calories, high in protein, folate and vitamins.

Since January and February are always crazy in the mornings for us, we always have a few quick and healthy breakfast options on rotation during the week. Hard boiled eggs, baked eggs and a batch or two of these easy Egg Muffins

BREAKFAST MUFFIN VARIATIONS

Looking for ways to switch up your eggs too? Today’s post features recipes and photos for 9 breakfast egg muffins that have been featured on Cooking Light and The Today Show.

These muffin cups are all:

• quick and easy to make in one bowl
• packed with protein and low in calories
• delicious as a healthy breakfast or a quick snack
• low carb
• keto-friendly
• great for meal prep
• simple to customize based on what ingredients you like or have on hand

You can find all of the healthy egg muffin recipes at the bottom of this post – or click on the link if there is one:

1. Broccoli and Cheese Breakfast Muffins with Eggs
2. Buffalo Chicken Egg Muffin Bake – Whole30 / Paleo / Dairy-Free
3. Ham and Cheese Egg Muffins
4. Jalapeno Popper Egg Muffins Keto
5. Kimchi Egg Muffins – recipe below
6. Bacon Egg Muffins
7. Spinach and Cheese Egg Muffins
8. Sun-Dried Tomato and Spinach Egg Muffins Paleo / Whole30 / Dairy-Free
9. Healthy Egg Muffins with Tomato and Spinach – Whole30 / Paleo / Dairy-Free

WHAT ARE EGG MUFFINS?

Breakfast muffins are like mini personal-sized omelettes or frittatas that you bake into a single-serving sized muffin tin or muffin cups.

They are very easy to make using simple pantry ingredients you probably already have in your pantry and fridge.

Egg muffins are perfect if you don’t have time for a proper sit-down breakfast and make a protein-packed breakfast for on the go.

WHY WE LOVE HEALTHY BREAKFAST MUFFINS:

Healthy muffins are not only delicious and easy to make, they are also:

• naturally gluten free
• paleo
• keto friendly
• Whole30 compliant

The best part is that you can make easy egg muffins ahead of time to have in the fridge for a quick breakfast or lunch!

ARE EGG MUFFINS KETO?

Yes. The macros for one breakfast egg cup (base recipe): 53 calories , 1 g Total Carb, 5 g Protein, 3 g Fat

WHAT INGREDIENTS DO YOU NEED TO MAKE BAKED EGGS:

• whole eggs (feel free to use more egg whites instead of whole eggs for a low calorie breakfast option)
• salt & pepper plus your favorite seasonings
• toppings of your choice

HOW TO MAKE EGG MUFFINS:

1. Start off by making your base recipe. It’s super simple and only contains THREE (3) ingredients.

• 10 large eggs (I used 10 whole eggs but you can try substituting  5 egg whites and 5 whole eggs if you prefer)
• 1 – 1 1/2 teaspoon salt (or to taste)
• 1/2 teaspoon black pepper (or to taste)

2. Whisk them together in a large 4-cup measuring cup or a mixing bowl. Add any other seasonings you like.

3. Chop up your favorite combo of vegetables and proteins and mix until combined.

4. Divide evenly among muffin cups (about 1/2 – 2/3 cups full) and sprinkle with any additional toppings.

I like lining my muffin tin with these silicone liners since they are guaranteed to pop out easily without sticking. Do not line with paper liners as they will stick.

If you don’t have silicone liners, it’s helpful if you grease the muffin tins with a non-stick cooking spray.

5. Pop the pan in the oven at 400 F and once cooled, you can store the egg cups in resealable bags or glass containers.

Keep them in the fridge (or freezer) and every morning, heat one up in the microwave for 30-40 seconds. Breakfast is ready to go!

CAN YOU BAKE EGGS IN THE OVEN?

Yes, absolutely. What I love about making baked eggs is that there is virtually no mess!

Plus, you can bake a batch on your Sunday or Monday meal prep day, wrap them up and store them in the freezer.

When you’re ready to serve, grab one of those single mini muffins (or two) and give it a quick reheat and you’re set to go!

ARE HEALTHY EGG MUFFINS KETO?

Yes, absolutely! Eggs are full of healthy protein and nutrients and very low in carbs. Plus, they fit perfectly if you are following a low carb, paleo, ketogenic or Whole30 diet.

With a batch of these egg muffin cups, now there’s no excuse to skip having a healthy breakfast when you’re on the run each morning. 

HELPFUL TIPS TO MAKE THE BEST EGG MUFFIN CUPS:

• Grease or line your muffin pan with silicone liners for easy removal
• Do not overfill – only fill each tin 1/2 – 2/3 full
• This recipe can be doubled for meal prep or to feed a crowd
• Use your favorite combo of vegetables or protein – be sure to chop them up into bite-sized pieces
• Since ham and sausage can tend to have a lot of fillers and extras, be sure to use a brand with less nitrates (Whole Foods or Trader Joe’s has a few great ones)
• Season with your favorite spices and herbs – not a fan of basil? Leave it out and use thyme or for an extra kick, cumin or Cayenne pepper instead.

9 EGG MUFFIN RECIPES:

The best part about making breakfast egg muffins is how easy they are to customize. I’m sharing 9 recipes here today but you can definitely make them all the same kind!

My kids love having different options for breakfast so I love switching up the add-ins and flavors. If you are dairy-free or want to make vegetarian egg muffins or paleo egg muffins, you can simply leave out the cheese or use a dairy-free cheese.

And then all you have to do is mix and match any protein, veggies and seasonings you like.

1. BROCCOLI AND CHEESE EGG MUFFINS

• eggs
• salt
• black pepper
• broccoli
• cheddar cheese
• garlic powder
• thyme

2. BUFFALO CHICKEN EGG MUFFINS PALEO / WHOLE30

• eggs
• salt
• pepper
• garlic powder
• cooked chicken
• green onions
• buffalo sauce

3. HAM AND CHEESE BREAKFAST EGG MUFFINS

• eggs
• salt
• pepper
• ham
• cheddar cheese
• garlic powder
• onion powder
• mustard (optional)

4. KIMCHI BREAKFAST EGG MUFFINS PALEO / WHOLE30

• eggs
• salt
• pepper
• toasted sesame oil
• chopped kimchi
• diced red bell pepper
• crumbled cooked bacon (optional)

5. JALAPENO POPPER BREAKFAST MUFFINS

• eggs
• salt
• pepper
• jalapenos
• bacon
• cream cheese
• cheddar
• garlic powder
• onion powder

6. BACON MUSHROOM & SPINACH EGG MUFFINS WHOLE30 / PALEO

• eggs
• salt
• pepper
• mushrooms
• spinach
• crumbled bacon

7. SPINACH AND PARMESAN CHEESE EGG MUFFINS

• eggs
• salt
• pepper
• spinach
• Parmesan cheese
• garlic powder

8. SUN-DRIED TOMATO AND SPINACH BREAKFAST EGG MUFFINS PALEO / WHOLE30

• eggs
• salt
• pepper
• sun-dried tomatoes
• spinach
• fresh basil

9. HEALTHY EGG MUFFINS WITH TOMATO & SPINACH EGG MUFFINS

• eggs
• salt
• pepper
• tomatoes
• spinach
• Italian seasoning
• garlic powder

HOW TO STORE EGG MUFFINS:

For an easy breakfast meal prep recipe, make a batch of egg muffins and store them fridge in a large zip-lock bag or an air-tight container for up to 4 days.

CAN YOU FREEZE EGG MUFFINS?

Yes! If you’re wondering how to freeze egg muffins, you would place them in a large zip-lock freezer bag or an air-tight container. You can store egg cups in the freezer for up to 3 months.

HOW TO REHEAT EGG MUFFINS:

To reheat egg muffins in the morning, simply take an egg muffin from the fridge or freezer. Place on a plate and reheat in the microwave on high for about 30 seconds.

You can also reheat the egg muffins in the air fryer or your oven at 375 F for about 5 minutes.

MORE EASY BREAKFAST RECIPES:

Breakfast egg muffins make busy mornings so much easier especially if you have earl risers in your house.

Having a few low carb breakfast recipes in your arsenal and ready to go first thing in the morning definitely helps. Here are a few more healthy breakfast ideas – there’s something for everyone:

• • Overnight Oats (8 Ways)
  • 12 Healthy Breakfast Cookies
  • Homemade Granola Bars
  • Low Carb Egg Casserole
  • Keto Avocado Egg Cups
  • 9 Low Carb Baked Egg Cups
  • Steel cut Oatmeal
  • 6 Delicious Steel Cut Oats
  • Old Fashioned Oatmeal
  • 10 Baked Oatmeal Cups
  • 12 No Bake Energy Bites

Pin HERE for later and follow me on Pinterest for more easy breakfast ideas

5 from 20 votes

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Breakfast Egg Muffins - 9 Low Carb Egg Cups

Prep Time

7 mins

Cook Time

15 mins

Total Time

22 mins

 

Breakfast Egg Muffin Cups - 9 Ways - 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!

Course: Breakfast

Cuisine: American

Keyword: breakfast egg cups, egg muffins, eggs, keto, low carb, make ahead, meal prep

Servings: 12 (a batch of 12 for each flavor)

Calories: 53 kcal

Author: Kelly

Ingredients

BREAKFAST EGG MUFFINS - START WITH THIS BASE FOR ALL FLAVORS FIRST:

• 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 Cheddar 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 Cheddar 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

Healthy Egg Muffins with Tomato & 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

START WITH THIS BASE RECIPE FOR ALL BREAKFAST EGG MUFFINS:

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

   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.

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.
   

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.

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.
   

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.
   

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.

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.

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.

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.

Healthy Egg Muffins with Tomato & 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.

Recipe Video

Nutrition Facts

Breakfast Egg Muffins - 9 Low Carb Egg Cups

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.