Breakfast Egg Muffin Cups (3 Ways!)

Super fluffy and loaded with your favorite fillings, these Breakfast Egg Muffins are so easy to make and still healthy for you! Eggs are whisked together, poured into a muffin tin, and then baked in the oven to make the cutest mini egg frittatas. This low-carb and keto egg cup recipe is a great base for a ton of filling options: bacon and cheddar, ham and Swiss cheese, or a veggie version with tomatoes and spinach!

Breakfast Egg Muffins Recipe

On-the-go or chilling at home, these egg muffin cups are one of the fastest and easiest breakfast recipes you can make. They also happen to be low carb!

They’re great for meal prepping ahead of time and reheating throughout the week on busy mornings.

You can double the recipe and feed a small crowd for Easter or Mother’s Day brunch.

Or just make them on a whim when you’re craving a fancy frittata in a cuter miniature version. (Yes, these egg muffin cups are essentially like mini frittatas!)

With this great base recipe you’ll find below, you can then get creative with whatever fillings you choose! And the best part is you will feel ready to tackle the day after eating these breakfast egg cups.

From more meat-heavy fillings like bacon and ham to a strictly vegetarian spinach egg muffin, there’s something here that everyone will love!

Egg Muffin Cup Ingredients

The basic ingredients you’ll need for these easy egg muffins are super simple to find:

• Eggs. You’ll need 10 large, whole eggs. Organic and pasture-raised eggs taste the best and are the healthiest option for you, but you can use whatever eggs you have on hand.
• Milk. Some type of milk will be mixed together to help fluff up the eggs. Cashew milk and almond milk have been tested in this recipe, but soy milk or regular milk may also be used.
• Garlic Powder. An absolute must! If you want, you can also whisk in two cloves of crushed garlic instead.
• Onion Powder. Not necessary, but this adds a nice little bite to counteract the savory fillings. You can also toss in some finely chopped onions if you’d prefer.
• Cheese. Some type of shredded cheese, such as cheddar cheese, Mozzarella, Swiss, or Parmesan cheese was used in all of these muffins. It’s not necessary to add cheese, so you can leave it out if you’re on a dairy-free diet.
• Meat. Cubed ham and crumbled bacon were mixed into two of the versions you’ll find below. You can also leave these out if you’re vegetarian and replace with additional vegetables.
• Vegetables. Tons of vegetables would taste great inside these egg frittata muffins. Chopped cherry tomatoes and thinly sliced fresh spinach were used in the muffins you see here, but you can also try green, yellow, or red bell pepper, onion, kale, green onions, red onions, and mushrooms.
• Herbs. Finely chopped fresh herbs brighten up the look and flavor of these egg muffins. Parsley and chives are great additions but thyme, rosemary, and oregano may also be used. Dried herbs can be replaced with fresh. Just make sure you reduce the amount used to ⅓.

Pro Tip: If using heartier vegetables, like potatoes, beets, or carrots, make sure you cook them partially before mixing in.

How to Make Breakfast Egg Muffins

One of the biggest obstacles most home-cooks run into when making breakfast egg muffins is that they end up sticking to the muffin tin.

This happened to me on numerous occasions. And the main culprit? The muffin pan I was using was old and no longer non-stick.

What is the best muffin tin for egg muffin cups?

In order to avoid a sticky egg mess, there are 2 types of muffin tins you can use:

• Non-stick muffin pan. The key here is to make sure it is still non-stick. If you see any scratches on your pan, or if you’ve had it for years and have made dozens of muffins in it, then it’s probably not as non-stick as you’d like. If this is the case, you can always buy a new non-stick muffin pan.
• Ceramic-coated muffin pan. This is probably the best option since it is the most non-stick of the pans. If you don’t already have one, this ceramic muffin pan is great.

Pro Tip: If you’re still nervous about your egg muffin cups sticking to the pan you can always use a parchment paper muffin cup liner. Do NOT use a regular paper liner as the eggs will stick mercilessly to it.

Decide on Fillings

One of the best things about making breakfast egg muffins is how versatile they can be! You can add in almost any filling ingredients you’d like. Here are some of the most popular filling options to try out:

• Bacon + Cheddar + Parsley
• Cubed Ham + Swiss Cheese + Chives
• Cherry Tomatoes + Spinach + Mozzarella

While the three filling options above are my go-tos, there are also numerous other fun ingredients you can throw in. Here are some other filling ideas for baked egg muffins:

• Ground Sausage, Chicken, Beef
• Artichokes, Eggplant, Bell Peppers, Broccoli
• Carrots, Potatoes, Sweet Potatoes (make sure to cook these before adding in.)
• Basil, Dill, Cilantro, Rosemary, Thyme

Whatever filling you choose, take a few minutes to prep them so you’re ready to add them to the muffin tin with the eggs.

Make the Egg Mixture

First, preheat your oven to 350°F. Be sure it has a time to completely warm up.

Add the eggs, milk, salt, pepper, garlic powder, and onion powder to a large bowl. You are going to beat this mixture, so be sure the bowl is big enough.

Use a whisk to thoroughly combine the ingredients.

Prep the Muffin Tin

Spray a 12-count regular-sized muffin tray with a good nonstick cooking spray. Completely coat each well so the eggs don’t stick to the sides or seams.

Pour the beaten eggs into each cup until they’re halfway full. If you go over this the muffins will puff up too much and deflate after baking.

Add the Filling and Bake

As good as eggs are, these are much better with your favorite filling ingredients.

Use a spoon or your fingers to add whatever you choose to each muffin cup.

Bake the egg muffins in the preheated oven for 22-24 minutes. When done, they should pull away from the sides and not jiggle in the middle.

Meal Prep and Storage

• To Prep Ahead: Egg muffins make a wonderful grab-and-go breakfast for busy weekdays. Simply bake the entire tray of muffins ahead of time and pull them out when you need them throughout the week!
• To Store: Store egg muffins in an airtight container in the refrigerator for up to 3-4 days.
• To Freeze: Wrap egg muffins individually in wax or parchment paper. Place in a freezer safe container or freezer bag and store for up to 2-3 months.
• To Reheat: Add egg muffins to microwave and cook for 30-45 seconds.

Can you freeze egg muffins?

Egg muffins freeze beautifully. Simply bake them according to the directions, allow them to completely cool in the fridge, then tightly wrap in a freezer-safe bag and store in the freezer for up to 2 to 3 months.

Can I make egg white muffins?

Yes, you can easily make egg muffin cups using only the egg whites. They are a great way to start your day with a low-carb, protein-packed breakfast. Make these Egg White Bites at home.

How do you keep egg muffins from deflating?

Inevitably, egg muffins will deflate some after baking. However, if you allow them to cool down inside the muffin tin this will prevent some of the drastic deflating that could happen.

Are egg muffins healthy?

These breakfast muffins are super healthy, especially when you stick with lean, nutrient-packed ingredients like spinach and tomatoes. As a word of caution, the more ingredients you add (like bacon and cheese), the higher the calorie and fat count goes.

How long do egg muffins last in the fridge?

Egg muffins are a great recipe to meal prep with because they easily last up to 3 to 4 days in the fridge when properly stored. Be sure to use an airtight container or tightly cover in plastic wrap.

Dietary Modifications

The recipe you’ll find below is already gluten-free and low-carb as written. Here are some adjustments you can make to help it fit your other dietary requirements:

• Vegetarian: Opt for a veggie-only filling. Leave out the meat products.
• Keto: Stick to lower-carb veggies, meat, and cheese fillings. Leave out the tomatoes, potatoes, or other starchy-vegetables.
• Paleo: Leave out the cheese.
• Whole30: Leave out the cheese and use sugar-free bacon.
• Dairy-Free: Leave out the cheese or replace it with a dairy-free option or cheese alternative.
• Nut-Free: Use regular milk or soy milk instead of a nut-based milk.

Expert Tips and Tricks

• Avoid the stick. Eggs have a tendency to stick to older and not-so-non-stick baking pans, so use a good, newer pan.
• Spray is a must. If you’re worried about your eggs sticking, non-stick cooking spray will do the trick!
• Cool off. Allowing egg muffins to cool in the muffin tin will prevent them from deflating too much.
• Give it a chop. Dicing all of the filling ingredients will ensure you have a bit of all of them in every bite.
• Use what you got! Chop up any leftover veggies, meats, or herbs you have in your fridge and throw them into your egg muffins for the week!
• Spice it up. Many blends, like Italian Seasoning, go great with this recipe to add flavor. Or, drizzle with your favorite hot sauce.

More Egg Breakfast Recipes

Start your day like a champion with an easy breakfast recipe that is not only tasty, but also healthy!

Sweet Potato Hash with Eggs and Breakfast Potato Hash with Bacon and Eggs are super simple to throw together and delicious recipes.

These Egg White Bites are a protein-packed breakfast and will have you skipping the Starbucks drive-thru line (and the egg yolks).

Get some Mexican flavor with Easy Migas Tacos or Breakfast Tostadas with Eggs.

Make a Shredded Hashbrown Casserole when you need to feed a crowd.

(If you still want to keep it low-carb but don’t want eggs, check out this Egg Free Keto Breakfast option!)