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Low Carb Breakfast Casserole (or Muffins)

This low carb breakfast casserole is healthy, packed with veggies, less than 30 minutes and adaptable to whatever you have on hand. It’s a great make ahead, freezer friendly, breakfast on-the-go.

The eggs and veggies are baked in the oven and can be made into muffins or a casserole. Instructions for both are in the recipe.

one square of egg casserole with veggies topped with tomatoes
veggie egg muffins stacked on plate

Casserole or muffin format? The muffins are super cute and make an awesome grab and go breakfast. But the casserole is easier I think, so you choose.

I just love the colors of the fresh veggies, especially the baby spinach. I don’t bother sautéing the vegetables before combining them with the egg mixture, but you can if you want for deeper flavor and less spongy eggs.

This low carb breakfast casserole is an easy recipe with simple ingredients. You can even make it in advance…which is great way to get a healthy breakfast on the table quickly on busy mornings.

What to expect

Versatility is the name of the game here for:

  • Ingredients: The core ingredients are eggs and cheese. The rest is pretty much up to your imagination. Veggies and/or meat.
  • Baking method: Bake in a single baking dish or as individual servings in a muffin tin. The egg casserole is similar to a frittata without the frying part.
  • How to enjoy them: Freshly baked, make ahead for meal prep or freezer option.

Nutrition

  • The dish is dairy free (if you add a dairy-free cheese), gluten free and perfect for a low carb or keto breakfast casserole recipe. I usually make a vegetarian version except when my son in law comes over.
  • This can be considered a healthy breakfast casserole with good protein from the eggs and cheese, good fiber and vitamins from the vegetables and some calcium from the cheese. It’s low carb and fairly low fat (as it’s baked in the oven).

Ingredients – tailored to your taste

cracked eggs in a bowl, spinach, bell pepper, parsley, grated cheese, green onion
Eggs, spinach, parsley, red pepper, grated cheese, green onion, seasonings

Variations to consider:

Here’s where you can pick and choose your faves or whatever you have on hand.

Vegetables: Use any of your favorite vegetables. I like green onions, fresh baby spinach and red bell peppers because of the color combination. Other good options are mushrooms, tomatoes with juices squeezed out, cooked sweet potatoes or zucchini. I suggest sautéing the mushrooms and zucchini first, though, because they have such a high-water content. Finely chop any vegetable you use.

Cheese: Use any combination of cheddar cheese, Monterey Jack, smoked Gouda, Swiss, Mozzarella or Pepper Jack cheese. You can also try feta cheese, goat cheese, parmesan cheese or ricotta.

Meat options: For a non vegetarian breakfast casserole, finely chopped cooked bacon, Italian sausage, breakfast sausage, chicken sausage and ham are all good options.

Herbs: Try fresh or dried basil, thyme, cilantro, oregano, parsley or dill.

Seasonings: You can add curry powder, garlic powder, taco seasoning, a pinch of smoked paprika, cayenne pepper, coriander or dried herbs. A tablespoon or so of olive tapenade would be amazing too if you like olives. I like to add 1/2 tsp of Dijon mustard to the egg mixture.

Step by step (for casserole and muffin format)

chopped veggies in processor bowl
Process veggies in a food processor until finely chopped. Include the cheese or add it after.
veggie egg mixture in bowl
Whisk eggs in a large mixing bowl. Add chopped veggie mixture with cheese and seasonings.

For a full-size casserole:

baked egg casserole in pyrex glass dish
Bake 17-19 minutes (for 7 x 11 pan/28×18 cm) or just until center no longer jiggles.
squares of egg casserole with veggies topped with tomatoes

For muffin cups:

veggie egg muffins stacked on plate
Top with fresh tomatoes and herbs if you like.

Tip

Should you add milk to the eggs? No. You might be used to adding whole milk or heavy cream to your scrambled eggs, but it’s not the best way. Milk doesn’t make fluffy eggs (as I used to think). In fact, adding milk dilutes the flavor and makes the eggs rubbery.

Recipe FAQs

What are the best types of eggs to buy?

According to Food and Nutrition, conventional eggs are perfectly fine. Pasteurized eggs are nutritionally the same as regular eggs, but but likely safer with lower risk of salmonella. Organic eggs are not better, just different in the amount of nutrients supplied. Cage-free, free-range certified organic eggs and pasture-raised eggs are not likely healthier or better, but you would be supporting humane farming practices.

Why is my egg casserole spongy?

The sponginess in the egg casserole is due to the combination of moisture from the eggs and added vegetables. To reduce the natural spongey texture of eggs, you can: 1) add a small amount of flour or cornstarch (about a tablespoon in this recipe) to the egg mixture 2) whisk less air into the eggs 3) precook the veggies.

How long does breakfast casserole last in the fridge?

As long as it is kept in the fridge, covered tightly with plastic wrap, it should stay fresh for between 4-5 days.

What to serve with a breakfast egg bake

For breakfast, I like to serve the squares with chopped tomatoes and avocado or some berries.

If you’re serving this egg casserole as part of a weekend brunch buffet, here are a few complementary recipes for your buffet table:

Shortcuts

  • Throw all the veggies you’re using into the processor to chop finely.
  • Buy pre-shredded cheese.
  • Buy pre-washed (and dried) fresh baby spinach.

Make ahead 

  • The low carb breakfast casserole can be prepped the day before and baked the following day. Or it can be fully cooked and kept in the fridge for up to 4-5 days. It can also be frozen for 2-3 months in an airtight container or bag.
  • Instructions for all 3 options and reheating are in the recipe below.
egg casserole with veggies topped with tomatoes

Love eggs?

Try our Gordon Ramsay scrambled eggs, sous vide poached eggs (with easy hollandaise). Or our classic egg salad recipe.

If you like this recipe, please leave a 5 star rating 🌟🌟🌟🌟🌟in the recipe card below. And if you REALLY like it, consider a review in the comments. Thanks very much!

one square of egg casserole with veggies topped with tomatoes
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Low Carb Breakfast Casserole (or Muffin Format)

This low carb breakfast casserole is healthy, packed with veggies, less than 30 minutes and adaptable to whatever you have on hand. It's a great make ahead, freezer friendly, breakfast on-the-go. Make it in casserole or muffin format.
Prep Time5 minutes
Cook Time18 minutes
rest time5 minutes
Total Time28 minutes
Course: Breakfast, brunch
Cuisine: American
Diet: Gluten Free, Low Calorie, Vegetarian
Servings: 6 muffins or squares

Ingredients

  • 6 large eggs
  • 1 cup fresh baby spinach, packed
  • 1 cup shredded or grated cheese I use half cheddar, half mozzarella
  • 1 green onion
  • 1/2 red pepper, cut into 3-4 pieces
  • 2 tablespoon chopped fresh parsley (or more) leave out if you don't have any on hand
  • Optional: chopped mushrooms, tomatoes; cooked ham, bacon or sausage; feta, Parmesan or goat cheese.

seasonings

  • 1/4 teaspoon salt (or more to taste)
  • 1/8 teaspoon garlic powder
  • 1/8 teaspoon ground black pepper
  • Optional: dried basil, red pepper flakes, fresh or dried thyme, dill, cilantro, 1/4-1/2 tsp Dijon mustard or more

Instructions

  • HEAT OVEN TO 350F/177C. Spray 7 x 11 pan (28×18 cm) or 8 x 8 pan (20×20 cm) with oil or line bottom with parchment for easy clean up. If doubling recipe, use 9 x 13 pan (22.5×32.5 cm). Note 1 for muffin format.
  • PREPARE EGGS: Crack eggs into a medium bowl. Add seasonings and whisk.
  • CHOP VEGETABLES: Add spinach, red pepper, green onion and parsley to food processor. Pulse until finely chopped. Add cheese and pulse 1-2 times to combine. Alternatively, finely chop vegetables. Add vegetable-cheese mixture to eggs.
  • FINISH CASSEROLE AND BAKE: Pour egg-vegetable mixture into prepared baking dish. If desired, sprinkle a little extra cheese on top. Place in oven and bake 17-19 minutes (for 7 x 11 pan/28×18 cm)) or just until center no longer jiggles. An instant read thermometer will be at 160F when cooked. If using a smaller pan, bake about 1-2 minutes longer. Let cool 5 minutes before cutting. Cut into 6 squares and serve. Note 2 to make ahead or freeze.

Recipe Notes

  1. To make egg muffins (instead of casserole): The ideal baking container is silicone muffin cups (6 cups), sprayed lightly as the egg muffins will pop right out. If you don’t have those, use a non stick muffin pan, sprayed with oil. Divide egg-vegetable mixture divide among the 6 muffin cups, filling no more than 3/4 full. Add a tsp extra cheese if desired on top of each cup. Bake 15-18 minutes or until set. Baking time will depend on the size of the muffin cups.
  2. Variations:
    • Vegetables: I use green onion, fresh baby spinach and red pepper because I love the color combination. Other good options are mushrooms, tomatoes, zucchini. I suggest sauteing the mushrooms and zucchini first, though, because they have such a high water content. Finely chop any vegetable you use.
    • Cheese: Use any combination of Cheddar, Monterey Jack, smoked Gouda, Swiss, Mozzarella. You can also try feta, goat cheese or ricotta.
    • Meat: Chopped cooked bacon, sausages and ham are all good options.
    • Herbs: Try fresh or dried basil, thyme, cilantro, oregano, parsley or dill.
    • Seasonings: You can add curry powder, garlic powder, taco seasoning, a pinch of smoked paprika, cayenne pepper, coriander or dried herbs. A tablespoon or so of olive tepanade would be amazing too if you like olives. I like to add 1/2 tsp of Dijon mustard to the egg mixture.
  3. Make Ahead:
    • For an overnight breakfast casserole: Make casserole. Cover tightly and place in fridge. Bake the next day. If cold from, fridge, casserole will need an extra few minutes to bake. 
    • To store in fridge after baking: Egg casserole can be stored in the fridge, covered, for 4-5 days. Slice and warm individual squares for 30 seconds in microwave. Or warm full casserole at 350F/177C, covered, for 15 minutes or until heated through.
    • To freeze, Cut casserole into squares and place them on flat pan in a single layer. Put in freezer to flash freeze for about 40 minutes. Transfer squares to a ziploc bag or airtight container to freeze for up to 2 months. To reheat, wrap individual square or muffin in paper towel and heat for 45 seconds in the microwave. Check, then add more time as needed in 10 second intervals. Once you know what works for you, memorize it for next time!
 
Nutrition value estimates are for 1 square (1/6 of pan) or 1 muffin, not including optional ingredients. 

Nutrition

Calories: 144kcal | Carbohydrates: 2g | Protein: 11g | Fat: 10g | Saturated Fat: 5g | Cholesterol: 183mg | Sodium: 282mg | Potassium: 135mg | Fiber: 1g | Sugar: 1g | Vitamin A: 1338IU | Vitamin C: 16mg | Calcium: 167mg | Iron: 1mg
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