Muffin Tin Eggs

Total Time
Prep: 15 min. Bake: 20 min. + standing

Updated on May 07, 2025

Muffin tin eggs are miniature baked omelets—perfect for meal prep. This version has a southwest flair, with tender mushrooms, spicy green chiles, savory ham and cheddar cheese tucked into each egg cup.

True story: I can’t keep up with the amount of scrambled eggs my family likes to eat for breakfast. Instead of cooking eggs on the stovetop every morning, make-ahead egg recipes are a lifesaver! This recipe for scrambled eggs in muffin tins yields 24 servings and freezes beautifully for an easy, nutritious on-the-go breakfast. All I have to do is pop a few in the oven or microwave to warm up while I sip my coffee, and breakfast is ready.

To make baked muffin tin eggs, start by whisking a big bowl of eggs. Then, stir in seasonings and mix-ins, pour the mixture into muffin tins and bake until the eggs are set. We’re using onion, mushrooms, canned green chiles, diced ham and shredded cheddar cheese to add flavor and texture to the eggs, but you can easily customize them with your favorite combination of meats, veggies and cheese.

Ingredients for Muffin Tin Eggs

  • Eggs: At first glance, the two dozen eggs this recipe calls for seem like a lot, but we’re baking 24 egg muffins, so it shakes out to one egg per muffin cup. Wondering which eggs to buy? As long as you use large eggs here, it doesn’t matter whether they’re labeled cage-free, free-range or organic (but I recommend learning the difference to choose the right eggs for your preferences!).
  • Seasoning: Garlic powder, salt and pepper give the scrambled egg mixture an extra-savory flavor. You’re not limited to these spices, though. See below for inspiration on how to customize the flavor with other seasonings and herbs.
  • Onion: A little chopped onion adds a savory, aromatic flavor to the egg bites. Dice the onion into small pieces so they cook through in the oven and won’t overpower the other flavors.
  • Mushrooms: Jarred or canned sliced mushrooms add an earthy flavor without the cook having to prep fresh mushrooms—just be sure to drain them first.
  • Green chiles: A small can of diced green chiles adds just the right amount of heat. There’s no need to drain them. Add the chiles with their juice, which is how this recipe was tested. For a non-spicy version, substitute finely chopped green bell pepper for the green chiles.
  • Ham: Diced deli ham adds smoky, meaty flavor and extra protein to these egg cups. For the best flavor and texture, I recommend picking up thick-cut deli ham—it’s meatier and more flavorful than thinly sliced deli meat.
  • Cheese: For bold, cheesy flavor, use sharp or extra-sharp cheddar. I recommend shredding a block of cheese yourself—it melts more smoothly and evenly than the bagged pre-shredded cheese.

Directions

Step 1: Prepare the egg mixture

Preheat the oven to 350°F. In a large bowl, whisk the eggs, salt, pepper and garlic powder until the eggs are beaten and the mixture is smooth. Stir in the mushrooms, green chiles, ham, onion and shredded cheese.

Editor’s Tip: Drain the mushrooms before mixing them with the eggs, but you can add the entire can of green chiles—the peppers and their liquid.

Step 2: Fill the muffin tins

Generously grease two standard muffin tins. Fill each muffin cup with roughly 1/4 cup egg mixture—you should have enough to fill all 24 muffin cups.

Editor’s Tip: Make sure to grease the bottom and sides of each muffin cup to prevent sticking. A pastry brush is the perfect tool to ensure every nook and cranny is well-greased.

Step 3: Bake

Bake the scrambled eggs in oven in muffin pans until the eggs are set, 18 to 20 minutes, rotating the muffin tins halfway through. Let the egg cups stand for 10 minutes before removing them from the pans. If desired, serve with pico de gallo.

Editor’s Tip: Insert a toothpick or paring knife into the center of an egg cup. They’re finished when the tool comes out clean and no liquid egg seeps out.

Table view shot of Muffin-Tin Scrambled Eggs; transfer on wire rack over a napkin; serve with pico de gallo; all set on white wooden surfaceALLISON CEBULLA FOR TASTE OF HOME

Recipe Variations

  • Please veggie lovers: Replace the ham, green chiles and/or mushrooms with vegetables. From asparagus to zucchini, you can use any assortment that makes you happy! Broccoli, bell peppers, leafy greens and tomatoes work well in egg recipes. Just be sure to dice them small so they distribute and cook evenly.
  • Try another meat: Instead of ham, you could add chopped chicken sausages, crispy bacon crumbles, browned chorizo or Italian sausage. Prefer meatless egg bites? Just omit the ham for a vegetarian-friendly version.
  • Experiment with seasoning: Give your baked scrambled eggs in muffin tins fresh flavor with a sprinkle of fresh or dried herbs, such as basil, parsley, dill, cilantro or chives. For something bolder, stir a teaspoon of ranch or taco seasoning into the eggs. Prefer some heat? Try crushed red pepper flakes or hot sauce.
  • Mix up the cheese: You can swap in any melting cheese, like Swiss or pepper jack. For a Mediterranean spin, try crumbled feta.

How to Store Muffin Tin Eggs

Let the baked eggs in muffin tins cool completely, then transfer them to an airtight container. Use parchment to separate layers and prevent sticking. The egg cups will stay fresh in the fridge for up to four days.

Can you freeze muffin tin eggs?

Yes, muffin tin eggs freeze well and can be reheated from frozen—perfect for grab-and-go breakfasts! Pack the egg cups into a freezer-safe container or wrap individual egg cups with storage wrap and place them in a resealable bag. They’ll last in the freezer for up to three months.

Can you make scrambled eggs in a cupcake pan ahead of time?

Absolutely! Baked scrambled eggs in muffin tins are the perfect make-ahead breakfast, especially for busy mornings. Whisk the eggs with your favorite mix-ins, pour the mixture into a muffin tin and bake. Let the egg cups cool completely before popping them out of the tin and into a storage container. Store them in the refrigerator if you’ll be eating them within a few days, or freeze them to make them last longer.

How do you reheat muffin tin eggs?

Microwaving is the fastest way to reheat the eggs, but you can bake them in the oven if you’re not in a rush. Place the egg cups on a microwave-safe plate, cover with a damp paper towel (it’ll prevent them from drying out) and nuke on high in 30-second intervals until warmed through. To bake them, preheat the oven to 350° and bake for 5 to 10 minutes or until warm.

Muffin Tin Egg Tips

Close-up shot of Muffin-Tin Scrambled Eggs; served on a plate with pico de gallo; a fork rest on a napkin; all set on white wooden surfaceALLISON CEBULLA FOR TASTE OF HOME

Should you use liners for baked eggs in muffin tins?

Muffin tin liners are optional. You can use them to make the scrambled eggs in muffin tins easier to remove and the pan easier to clean, but liners can also keep the edges of the egg muffins from turning crispy and golden in the oven. To keep the eggs from sticking to the muffin tins, I recommend spraying your pans with nonstick spray or generously coating them with neutral oil or butter.

How long does it take to cook eggs in a muffin tin?

These egg muffins take about 20 minutes to bake in a 350° oven. Since every oven heats differently, I recommend checking them for doneness after 16 to 18 minutes. The eggs are ready when set in the center and lightly golden around the edges. You can double-check their doneness by sticking a toothpick or the tip of a knife into the center of one—if it comes out clean and dry, they’re good to go!

Can you cook plain eggs in a muffin tin?

Yes, you can cook plain eggs, scrambled or unscrambled, in a muffin tin. Grease your pan well, then crack one whole egg into each muffin cup and bake at 350° for about 15 minutes, until the egg whites are set and the yolks are to your liking. To make plain baked scrambled eggs, simply whisk the eggs before filling the muffin tin.

Watch How to Make Muffin-Tin Scrambled Eggs

Muffin-Tin Scrambled Eggs

Prep Time 15 min
Cook Time 20 min
Yield 2 dozen

Ingredients

  • 24 large eggs
  • 1 teaspoon salt
  • 1/2 teaspoon pepper
  • 1/4 teaspoon garlic powder
  • 1 jar (4 ounces) sliced mushrooms, finely chopped
  • 1 can (4 ounces) chopped green chiles
  • 3 ounces sliced deli ham, finely chopped
  • 1/2 medium onion, finely chopped
  • 1/2 cup shredded cheddar cheese
  • Pico de gallo, optional

Directions

  1. Preheat oven to 350°. In a large bowl, whisk eggs, salt, pepper and garlic powder until blended. Stir in mushrooms, chiles, ham, onion and cheese. Spoon about 1/4 cup mixture into each of 24 greased muffin cups.
  2. Bake until eggs are set, 18-20 minutes, rotating pans halfway through baking. Let stand 10 minutes before removing from pans. If desired, serve with pico de gallo.

Nutrition Facts

1 egg cup: 88 calories, 6g fat (2g saturated fat), 190mg cholesterol, 257mg sodium, 1g carbohydrate (0 sugars, 0 fiber), 8g protein. Diabetic Exchanges: 1 medium-fat meat.

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I made these one year at Christmas as a way to save time, and they were a big hit. I have to make a large batch because my husband and boys can polish them off in a short amount of time. These also freeze very well, if there are any left! —Jill Darin, Geneseo, Illinois
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