These savory Breakfast Muffins can be made with the vegetables, cheese and meat you like best. Serve these little egg muffin cups on a brunch buffet, or freeze to reheat for a convenient weekday breakfast.

A white plate topped with breakfast muffins made with eggs, bacon, veggies, cheese and herbs.

These Egg Muffin Cups are the best make-ahead morning meal!

When it comes to weekday breakfast, prepping ahead is key for my family. We love anything that’s grab-and-go to get some nourishment on groggy mornings.

We turn to these Breakfast Muffins several times a month. They can be made in advance, kept in the freezer for a month, and reheated in a flash.

They’re delicious and nutritious, because they can be packed with all kinds of vegetables!

Why you will love these egg muffins:

  • Versatile. Make them with whatever veggies, cheese and breakfast meat you have on hand.
  • Lots of protein from the eggs and cheese to keep you going throughout the day.
  • So quick to reheat! We’re talking 30 to 45 seconds in the microwave, max!

“This was a positively delicious recipe.  It is so healthy and worth every minute of putting it together.”

—Donna
Ingredients laid out on a light surface, including eggs, mushrooms, a red bell pepper, bacon, cheese, herbs and spices.

Egg Muffin Recipe ingredients:

  • eggs – you will need 8 large eggs to make 12 make ahead breakfast muffins.
  • milk – this stretches the eggs further, and adds a touch of creaminess to this breakfast muffin recipe.
  • Cheddar cheese – creates gooey pockets of cheese in the muffin cups!
  • bacon – I started with my bacon in the oven recipe, and crumbled it, before starting my muffins. Save the grease for bacon gravy on the weekend.
  • red bell pepper – this provided a pop of color and sweetness.
  • mushrooms – I used thinly sliced cremini (baby bella) mushrooms here, but white button mushrooms work, too.
  • parsley – this adds a burst of herby flavor and brightens up the dish.
  • salt and pepper – for seasoning the egg mixture for this egg muffin recipe.
  • nutmeg – I think that a pinch of nutmeg adds a certain something something to any baked egg dish.
  • nonstick cooking spray – for coating the muffin pan so the egg cups slide right out.

Types of breakfast muffins

In the recipe below, I’ve listed the ingredients I like best for these make ahead breakfast muffins. But the best thing about this breakfast muffin recipe is how adaptable it is.

  • If turkey bacon is more your speed, check out my tutorials on how to cook turkey bacon in the oven and turkey bacon in an air fryer use that instead of regular bacon.
  • You could also use crumbled breakfast sausage or chopped up ham in this egg muffins recipe. Or, you can simply leave the meat out altogether.
  • Instead of mushrooms and red pepper, you could use spinach, onions, sundried tomatoes, or any other veggies you have on hand.
  • If you don’t have Cheddar cheese, just about any type of cheese will work here! I’ve tried this with everything from feta to Monterey Jack to goat cheese, and it turns out great every time. Crumble any crumbly cheese instead of shredding it, of course.
Chopped mushrooms and red bell peppers being sauteed in a stainless steel skillet.

How to make Egg Muffins

  1. Preheat the oven and saute the veggies. Whatever veggies you use, saute them long enough so that they are softened before you put them into the egg muffins.
  2. Whisk the eggs and add the milk and seasonings to them.
  3. Prepare your muffin pan and divide your veggie mixture between the cups.
  4. Sprinkle the cheese and bacon over the veggies.
  5. Divide the egg mixture between the cups.
  6. Transfer the pan to the oven and bake until the eggs are set.
  7. Let the muffins cool on a wire rack for 5 minutes, and then remove the muffins from the pan. You may need to run a small knife around the outside of each cup to loosen the muffins.

How long to bake egg cups

In a preheated 375 degree F oven, the egg muffins should take about 15 minutes to bake until their centers are set.

But remember, all ovens and all muffin pans are a little different, so your cooking time may vary by a few minutes.

A large glass measuring cup with a yellow liquid topped with herbs and spices.

Home Chef Tips for Breakfast Muffins

  • After many tests, I’ve found that PAM brand original canola oil blend cooking spray works the best for this recipe. I’ve tried it with fancier all-olive oil cooking sprays, and my muffins stuck to the pan a little bit.
  • If you have an instant-read thermometer, use it for this egg muffins recipe! You’re looking for a temperature of about 170 degrees F in the center of each muffin for a perfectly set egg cup.
A 12-cup muffin pan filled with egg muffin cups made with bacon, cheese and veggies, unbaked.

How to serve Breakfast Egg Muffins

Serve these egg muffin cups on their own for an easy on-the-go meal, or pair them with a salad for Easter, hash browns, or Fall fruit salad for a well-rounded breakfast.

A 12-cup muffin pan filled with breakfast egg muffins made with bacon, cheese and veggies, fully baked.

Storing Breakfast Muffins

These make ahead breakfast muffins can be made and served immediately, or made in advance to eat later.

Can you leave egg muffins out overnight?

No, unlike traditional muffins like cranberry muffins, egg muffins will spoil at room temperature. They need to be refrigerated or frozen after they cool to room temperature.

How long can you keep egg muffins in the fridge?

One cooled, egg muffins can be stored in an airtight container or zip-top bag in the refrigerator for up to 3 days.

Egg muffins made with bacon, cheese and veggies piled up on a white plate.

Can you freeze egg muffins?

Absolutely! One cooled, egg muffins can be stored in an airtight container or zip-top bag in the freezer for up to 1 month.

Can you reheat egg muffins?

Yes, it’s recommended!

In less than a minute, these breakfast egg muffins can be microwaved for a hot and tasty homemade breakfast.

Brunch muffins can be re-heated in a microwave straight from the refrigerator or freezer. Place as many as you want to eat on a microwave-safe plate and microwave 30 to 45 seconds or until heated through.

Two egg muffin cups on a white plate, with one of them having been cut in half, exposing the veggies inside.

Breakfast Muffins Recipe FAQS

Why are my egg muffins watery?

Overcooking the egg muffins or using too much milk can lead to a watery consistency. Make sure you measure the milk carefully for this breakfast muffins recipe.

Why are my egg cups rubbery?

Overcooking can case the eggs to become rubbery. Be sure to bake the breakfast egg muffins until they are just set, but no longer.

How do you keep eggs from sticking to muffin pans?

Use PAM brand original canola oil blend cooking spray for best results with this egg muffin recipe.

Why did my egg muffins turn green?

Certain eggs contain a bit more vitamin B12, which means that the white of that egg can have a greenish tint. It’s not harmful at all. In fact, extra vitamins in your egg muffins is good for you!

Egg muffins made with bacon, cheese and veggies piled up on a white plate.
A white plate topped with breakfast muffins made with eggs, bacon, veggies, cheese and herbs.

Breakfast Egg Muffins

Yield: 12 muffins
Prep Time: 20 minutes
Cook Time: 18 minutes
Additional Time: 5 minutes
Total Time: 43 minutes

These savory Breakfast Muffins can be made with the vegetables, cheese and meat you like best. Serve these little egg muffin cups on a brunch buffet, or freeze to reheat for a convenient weekday breakfast.

Ingredients

  • 1 tablespoon olive oil
  • 4 ounces cremini (baby bella) mushrooms, chopped
  • 1/2 red bell pepper, finely chopped
  • 8 eggs
  • 3/4 cup milk
  • 2 tablespoons chopped fresh parsley
  • 1/2 teaspoon kosher salt
  • 1/4 teaspoon ground black pepper
  • Pinch ground nutmeg
  • Nonstick cooking spray (PAM brand works best)
  • 6 slices oven bacon, crumbled
  • 2 cups (8 ounces) shredded Cheddar cheese

Instructions

  1. Preheat oven to 375 degrees F. Heat oil in large skillet over medium heat. Add mushrooms and bell pepper to skillet and cook 3 to 4 minutes or until softened, stirring occasionally. Remove from heat.
  2. Meanwhile, in large liquid measuring cup, whisk eggs until well beaten. Whisk in milk, parsley, salt, pepper and nutmeg.
  3. Liberally spray a 12 cup standard muffin pan with cooking spray. Divide vegetable mixture between prepared muffin cups. Divide bacon and cheese evenly over vegetables, then pour egg mixture evenly over all of the cups.
  4. Transfer to oven and bake 14 to 16 minutes or until eggs are set. Transfer pan to wire rack and let stand 5 minutes. Run small knife around outside of each cup to remove muffins. Serve immediately, or transfer muffins to wire rack and let cool completely, then transfer to zip-top bags and refrigerate or freeze for later use. 
  5. Muffins can be refrigerated for up to 3 days or frozen up to 1 month. Muffins can be re-heated in microwave straight from refrigerator or freezer. Place on microwave-safe plate and microwave 30 to 45 seconds or until heated through.

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Nutrition Information:
Yield: 12 Serving Size: 1 muffin
Amount Per Serving: Calories: 172Total Fat: 13gSaturated Fat: 6gTrans Fat: 0gUnsaturated Fat: 6gCholesterol: 150mgSodium: 328mgCarbohydrates: 2gFiber: 0gSugar: 1gProtein: 11g

This website provides estimated nutrition information as a courtesy only. You should calculate the nutritional information with the actual ingredients used in your recipe using your preferred nutrition calculator.

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