Skinnytaste > Recipes > Meal Prep Recipes > Loaded Egg Muffins

Loaded Egg Muffins

This post may contain affiliate links. Read my disclosure policy.

Fill these easy loaded egg muffins with any combination of veggies, cheese, and meats. Perfect breakfast to make ahead for the week.

Loaded Egg Muffins

Loaded Egg Muffins

These healthy Loaded Egg Muffins are made with eggs, bacon, spinach, cheese, and veggies and then baked in a muffin tin. I used some of my favorite omelet ingredients, but you can switch it up and use whatever you like or have in your fridge. More of my favorite egg muffin recipes are these Broccoli and Cheese Egg Muffins, Egg White Muffins, and Hash Brown Egg White Nests.

Loaded Egg Muffins

Why This Recipe Works

  • Healthy: Two omelet muffins have 14 grams of protein with only 165 calories and under three grams of carbs.
  • Meal Prep: These egg cups are perfect for making ahead whenever you have time, and they freeze and reheat well.
  • Convenient: They’re a great grab-and-go breakfast or snack to have ready in the fridge or freezer.

Loaded Egg Muffin Ingredients

  • Eggs: You’ll need nine large eggs.
  • Salt and Pepper to season
  • Vegetables: Thawed and drained frozen spinach, tomatoes, onion, bell pepper
  • Bacon: Cook three strips of bacon and chop it.
  • Cheese: Use two ounces of shredded cheddar, or mozzarella, swiss, etc

How to Make Egg Muffins

  1. Once all your ingredients are prepped, these easy egg muffins come together quickly. Just whisk the eggs, season with salt and pepper, and stir in the remaining ingredients.
  2. How to Bake Eggs in Muffin Tin: Preheat the oven to 350°F, and spray a muffin tin generously with cooking spray. Place the tin on a baking sheet and pour in the egg mixture.
  3. How Long to Bake Egg Muffins: Bake at 350°F for 20 to 25 minutes until set. When you pull them out of the oven, they may deflate a little – this is normal!

To prevent egg muffins from sticking to the tin, follow these steps:

  1. Properly Grease Your Muffin Tin:Use an olive oil spray to thoroughly grease each muffin cup, including the sides and bottom.
  2. Use Silicone Muffin Cups:Consider using silicone cups or liners, which are naturally nonstick.
  3. Allow Egg Muffins to Cool Before Removal: After baking, let the omelet muffins cool for at least five to 10 minutes. Cooling allows the egg to retract slightly from the sides of the tin, making them easier to remove.
  4. Use a Knife or Spatula:If they are still stuck after cooling, use a thin knife or a small spatula to carefully loosen the edges of each egg muffin before attempting to remove them from the tin.

How long do egg muffins keep?

Egg muffins are perfect for meal prep. You can even double the recipe. Make them ahead and freeze or refrigerate the rest. They will keep in the refrigerator for up to four days.

How to Freeze

Here’s what to do to freeze these breakfast muffins for the month:

  • Let the muffins cool, then remove them from the muffin tin.
  • Flash freeze them by setting them on a parchment-lined baking sheet and sticking the pan in the freezer. This step prevents the muffins from freezing together.
  • Once frozen, transfer them to a freezer-safe bag, label it, and return it to the freezer.

How to Reheat Egg Muffin Cups

To reheat, you don’t even have to thaw them first. Pop them in the microwave straight from the freezer and warm for one minute until heated through.


You can fill these breakfast egg muffin cups with anything you like in your omelets! Below are some variations:

  • Eggs: If you prefer egg whites, you can use them or do half eggs and half whites.
  • Cheese: Omit the cheese to make them Paleo or Whole30. Or swap the cheddar with Monterrey Jack, mozzarella, or Swiss.
  • Vegetarian Egg Muffins: Omit the bacon.
  • Meat: Add chopped, cooked chicken sausage or ham.
  • Don’t like one of the veggies? Missing one? No worries! Swap any of the vegetables for whatever you like. Zucchini, mushrooms, asparagus, and broccoli would all be good.
  • Leafy Greens: Use leftover cooked leafy greens, like Swiss chard or kale. If you don’t have frozen spinach, sauté fresh and add it to the muffins.
  • Western Omelet: Use ham, Swiss, and bell peppers.
  • Egg Casserole: You can bake the egg mixture in an 8”-x-8” pan for about 30-40 minutes. Check it with a toothpick to ensure it’s clean before removing it from the oven.
Loaded Baked Egg Muffins

More Egg Muffin Recipes

Loaded Egg Muffins

4.69 from 122 votes
These easy, loaded egg muffins can be filled with any combination of veggies, cheese and meats. Easy breakfast to make ahead for the week.
Course: Breakfast, Brunch
Cuisine: American
Loaded Baked Egg Muffins
Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes
Yield: 6 servings
Serving Size: 2 omelets


  • nonstick muffin pan


  • nonstick cooking spray
  • 9 large whole eggs
  • 1/4 teaspoon kosher salt
  • black pepper, to taste
  • 3 tablespoons thawed frozen spinach, drained
  • 3 tablespoons diced tomatoes
  • 3 tablespoons diced onion
  • 3 tablespoons diced bell pepper
  • 3 strips cooked bacon, chopped
  • 2 ounces shredded cheddar


  • Preheat the oven to 350F. Spray the muffin tin generously with cooking spray to prevent sticking.
  • In a large bowl whisk the eggs, season with salt and pepper.
  • Mix in the remaining ingredients.
  • Fill  and place tins on a cookie sheet and bake 20 to 25 minutes, until set.

Last Step:

Please leave a rating and comment letting us know how you liked this recipe! This helps our business to thrive and continue providing free, high-quality recipes for you.



Serving: 2 omelets, Calories: 165 kcal, Carbohydrates: 2.5 g, Protein: 14 g, Fat: 11 g, Saturated Fat: 4.5 g, Cholesterol: 289 mg, Sodium: 267 mg