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Start your new healthy lifestyle with these free recipes & Tips

You’ll get immediate access to your download with simple shifts you can start today—because every small habit tweak helps.

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Healthy Breakfast Egg Muffins Recipe

Healthy Breakfast Egg Muffin Recipe Elizabeth Rider-4

Healthy breakfast egg muffins are here for the win!

Not only are they easy, but they’re also healthy if you make them right.

Egg muffins are super flexible and a great way to use up extra veggies. They’re essentially mini frittatas (or little crustless quiches), and make a great make-ahead meal for something nutritious when you’re on the go or just simply not in the mood to cook. Whip up a big batch on Sunday to have a healthy breakfast all week long.

How to Make Healthy Breakfast Egg Muffins

The Eggs

To make your egg muffins healthy, use the highest quality eggs you can find and be sure to include a lot of veggies. I prefer organic pasture-raised eggs. Skip the highly-processed ham and bacon (I use turkey bacon here) and go easy on the cheese if you use any at all.

When it comes to the eggs, I like to use 2 whole eggs to one egg white for extra protein and to make these a little lighter. Again, this is a personal preference, so use whole eggs if you prefer.

In general, you’ll need about 1 egg per egg muffin you want to make, and about 1 cup total of any combination of finely chopped cooked veggies & filling per 6 egg cups (don’t worry, I did all of the math for you in the printable recipe below!).

The Veggies & Filling

In this recipe below, I used some leftover organic turkey bacon that I had made for some guests over the weekend. I think this might be my first recipe ever posted here with turkey bacon—I’m not a huge meat eater but really like it in this recipe.

You have so many options when it comes to filling. I added 2 slices of chopped cooked turkey bacon and 1/4 cup grated real Parmigiano Reggiano cheese (something else I don’t use often!) Real Parmigiano Reggiano is a high-quality hard cheese that comes from Italy. Its production is regulated to be sure it’s clean with no additives, and the way it’s fermented makes it almost 100% lactose-free. I don’t eat a lot of dairy but find real Parmigiano Reggiano easy to digest so I use it occasionally. If you want your egg muffins to be completely dairy-free just leave it out, and omit the turkey bacon if you’re not into that either.

Egg muffins will puff up above the muffin tin while baking, then settle back once out of the oven, so fill each muffin tin about three-quarters of the way full to account for that. Bake them at 375F° for 15 minutes (give or take a minute or two depending on your oven) until a toothpick comes clean out of the middle.

Easy Clean-Up

And the last note, use unbleached muffin papers or silicone muffin holders for easy cleanup. You can make them directly in a muffin tin sprayed with extra virgin olive oil spray, but I find that to be more mess to clean up than it’s worth. In the images here, I didn’t use them, but used them the next time I made them and the muffin papers are worth it! I get the unbleached ones at the natural foods store that are basically just parchment paper.

Healthy Breakfast Egg Muffin Recipe Elizabeth Rider

Wait, are eggs healthy?

I get this question all. the. time.

Here’s my take: the only way to know if a food works for you is to eliminate it for at least 21 days, then add it back in and see how you feel. I’ve eliminated eggs a few times over the last few years as recommended in a protocol for reactivated Epstein-Barr, and when I add them back in I still feel great. In short, you have to try and test different foods to see if they work with your biology.

Eggs are a whole food and rich source of protein (in the egg whites) and nutrients like choline (in the yolk). The nutrition community used to think that dietary cholesterol, like that found in eggs, would directly affect our blood cholesterol, but that myth has been widely debunked. We now know that levels of blood cholesterol are more impacted by excessive amounts of sugar and highly-refined carbohydrates than whole real foods like eggs. When in doubt with eggs (or any food), eliminate it for 21 days—be diligent because a true elimination requires that you have absolutely none of the food—then add it back in and see how you do. You can read more about this and get a more detailed protocol in my book, The Health Habit.

For now, I’m on eggs and feeling great!

Healthy Breakfast Egg Muffin Recipe Elizabeth Rider-4

Healthy Breakfast Egg Muffins



  • extra-virgin olive oil spray*
  • 1 small shallot, finely diced
  • 1 cup broccoli florets, finely chopped
  • 1/2 cup button or cremini mushrooms, finely chopped
  • 2 slices cooked turkey bacon, chopped (optional)
  • 8 large eggs, plus 4 egg whites from 4 eggs
  • 1/4 cup unsweetened almond milk
  • 1/4 cup real Parmigiano Reggiano cheese, grated (optional, use the real stuff to avoid preservatives)
  • 1/2 teaspoon fine sea salt (I use Real Salt, use a scant half teaspoon if using turkey bacon)
  • a few spins freshly ground coarse black pepper


  1. Preheat the oven to 375F°. Line a 12-cup muffin tin with unbleached muffin papers or silicone muffin holders.
  2. In a medium saute pan sprayed with extra virgin olive oil spray (or a small drizzle of extra virgin olive oil), saute the shallot over medium heat for 2 minutes. Add the chopped broccoli and chopped mushrooms (and any other veggies you’re using) and saute until soft, 6-8 more minutes. Add a sprinkle of sea salt and pepper to the pan while the veggies saute.
  3. While the veggies cook, in a medium mixing bowl, whisk the eggs, egg whites, unsweetened almond milk, Parmigiano Reggiano (if using), 1/4 teaspoon sea salt and a few spins of black pepper until well combined into a uniform mixture, about 30 seconds.
  4. Remove the veggies from the heat and mix in the chopped turkey bacon if using.
  5. Spray the insides of the muffin papers with extra virgin olive oil spray to be extra sure they come out nicely. Add about 2-3 tablespoons of the veggie and turkey bacon mixture to each muffin spot. Pour the egg mixture over the veggies about 1/2 of the way up each slot.
  6. Bake for 15-17 minutes until a toothpick comes clean out of the middle of an egg cup. The egg muffins will puff up in the oven, then settle back after taken out of the oven. Let cool at least 10 minutes before serving. Will keep in the refrigerator in an airtight container for up to 3 days. These can be frozen up to 3 months if needed, however, I think they’re better when not frozen.


* If using extra virgin olive oil spray, be sure to read the ingredients and only use a spray that is just extra virgin olive oil. I use the 365 brand one from Whole Foods. Avoid sprays with propellants or additives. If you don’t have a spray, a small drizzle of extra virgin olive oil works great.

Note: the recipe above makes enough for 12 regular size egg muffins. Halve the recipe for a 6-cup muffin pan or a 12-cup mini-muffin pan.

Healthy Breakfast Egg Muffin Recipe Elizabeth Rider-3

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  1. Susan M. says:

    Sounds wonderful as I am looking for easy breakfast for a crowd over the holiday. How would I reheat not to dry out? Thanks so much for all the great recipes!

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