Keto Low-Carb Breakfast Bacon and Cheese Egg Muffins (Bites) + VIDEO

These Keto Low-Carb Egg Muffins are quick and easy to make for your meal prep breakfast. These cups are loaded with bacon, cheese, and veggies and are freezer-friendly and great for an on-the-go snack.

This post contains affiliate links. Please read my full disclosure here.

This post was originally published in 2018. It has since been updated.

These muffin bites are great for batching and freezing for later.

What Are Egg Muffins

They are mini omelets that you can bake in muffin tins. The bites are freezer friendly and great for meal prep when you don’t have a lot of time to prepare breakfast in the mornings.

How to Make Keto Egg Muffins (Bites)

Detailed measurements and full instructions can be found in the recipe card at the bottom of this post.

  1. Whisk eggs in a large bowl with salt and pepper to taste.
  2. Spray a 12-capacity muffin tin with cooking oil.
  3. Pour the eggs into each tin, only fill each about halfway.
  4. Add in meat and vegetable toppings.
  5. Top with the shredded cheese.
  6. Bake.

Cook Time/How Long to Cook

The total bake time is around 15 minutes. You want to cook the eggs until they are nice and fluffy and aren’t overcooked. Overcooked eggs will taste rubbery and dry.

How to Get Fluffy Eggs

The cheese will help keep the omelet muffins fluffy. They will also stay fluffy if you don’t overbake and overcook the eggs.

Additional Substitution and Add-Ins

  • Sausage
  • Ham
  • Shrimp
  • Crab
  • Mixed Greens
  • Kale
  • Caramelized Onions
  • Fresh Herbs
  • Asparagus

How to Store/How Long Will They Last?

The egg muffins should keep for 1 week in the refrigerator. I usually shoot for 5 days.

How to Reheat

I like to use the microwave for 25-30 seconds. You can also use a toaster oven.

Can You Eat Them Cold?

Yes, you can eat them cold. I prefer to heat them while warm with melted cheese.

Freezer Tips

Absolutely! These egg muffins freeze well. You can freeze them tightly covered and sealed for 3 months. Defrost overnight in the fridge.

More Egg Recipes

Egg White Frittata

Bacon, Egg, Cheese, and Spinach Breakfast Casserole

Sous Vide Egg Bites Bites

Keto Low Carb Egg Salad

Low-Carb Breakfast Ideas:

Keto Chaffles (Waffles)

Keto Cinnamon Rolls

Keto Blueberry Muffins

Click here for a complete listing of Keto Low-Carb Recipes.


  • 12 eggs
  • salt and pepper to taste
  • 6 slices of Butcher Box bacon, cooked and crumbled
  • 1/2 cup onion, chopped
  • 1/2 cup chopped green pepper
  • 1/2 cup chopped red pepper
  • 1/3 cup chopped mushrooms (any type you prefer)
  • 1/2 cup shredded mozzarella cheese
  • 1/2 cup shredded cheddar cheese, I used smoked cheddar cheese
  • 1/2 cup fresh spinach, finely chopped


  1. Preheat oven to 350 degrees.
  2. Whisk the eggs in a large bowl with the salt and pepper to taste.
  3. Spray a 12 capacity muffin tin with cooking oil. I like to use olive oil.
  4. Pour the eggs into each tin, only fill each about halfway.
  5. You can toss the bacon, onions, peppers, and mushrooms in a bowl if you like, to mix them up and add them to each of the tins. Or you can just divide each equally into each of the muffin tins. Place the veggies on top of the eggs.
  6. Top with the shredded cheese.
  7. Bake for 14-16 minutes or until the eggs are set. Mine were ready at 16 minutes. If you like your eggs more firm, give them additional time.
  8. Cool completely before serving. If you remove the egg bites too soon the edges of the bites will be left behind in the muffin tin.


This recipe makes 12 egg bites. Divide the ingredients in half for less egg bites.

Instead of buying pre-shredded cheese I purchase block cheese and shred it with a cheese grater. It melts and tastes so much better than pre-shredded!

Feel free to use any flavor of cheese you wish.

These bites are freezer friendly. I defrost them overnight before use.

The bites will keep in the refrigerator for 5 days.

Recipe update:

I’ve found it’s much cleaner and easier to make this recipe using silicone muffin mold liners. Eggs usually stick the muffin tin. These don’t stick to the silicone and are much easier to clean.

Nutrition Information

Yield 12 egg muffins

Serving Size 1 egg muffin

Amount Per Serving

Calories 144Total Fat 11gCarbohydrates 2 netgProtein 10g

Read More

Thanks! You've already liked this
No comments