These Ham and Cheese Egg Cups are made with just 3 main ingredients, deli ham, cheddar cheese, and eggs, plus a few simple seasonings. I love them for busy mornings when everyone needs something filling, but nobody has time for a sit-down breakfast. These oven-baked egg cups are packed with protein, low-carb, keto-friendly, and gluten-free. Just 12 minutes in the oven and breakfast is done!

I’ve always made my egg muffins for meal prep breakfasts, but then I tried these ham egg cups. And wow. What a fun way to switch up the routine! Unlike egg muffins, these keep the egg whole, so you can get a soft, jammy egg moment in a grab-and-go breakfast. I bake mine for 12 minutes, which gives me set whites, melty cheese, crisp ham edges, and a runny yolk; 15 minutes will give you firmer yolks and even crispier ham. Either way, you’ll know they’re ready when the egg whites look opaque, and the ham cups are lightly browned around the edges. These cheesy ham egg cups are quick enough for weekdays, but cute enough to serve for brunch too!

Helpful Tips & Variations

• Spray the muffin tin well. The ham sometimes sticks to the pan as it bakes. A light coating of cooking spray helps the egg cups lift out cleanly without tearing.
• Use the standard sliced ham. Deli ham works best here, but I’d avoid super thin slices since they can rip when you press them into the muffin tin. Average-thickness slices hold their shape better and make a sturdier little cup. I love smoked ham for the extra savory flavor.
• Add a few veggies, if you like. A little sliced green onion, small diced red bell pepper, or chopped spinach can be added to the ham cups with the cheese. Just don’t overfill them to avoid overflowing when you add the eggs.
• Switch up the cheese. I like sharp cheddar for a sharper, tangier cheese flavor, but mild cheddar is nice too, and tastes creamier. Other melty cheeses will also work here. Monterey Jack melts really well and keeps things mellow, Swiss adds a nutty flavor, and pepper Jack gives them a little kick.
• Shred the cheese yourself if you can. Freshly shredded cheese melts smoother than pre-shredded cheese, as it usually has additives to keep it from clumping in the bag. Bagged cheese will still work, but freshly shredded gives you a better melty layer under the egg.
• Watch the bake time. I use large eggs for this ham egg cup recipe, so the timing is based on that size. Since every oven runs a little differently, start checking around 12 minutes if you like a softer center, or leave them in a few minutes longer if you want the yolks more set, closer to hard boiled eggs. The ham edges also get crisper the longer they bake (which my family definitely doesn’t complain about!)

How to Make Ham and Cheese Egg Cups Step by Step

Gather all of your ingredients. Preheat your oven to 400°F and place a rack in the center position so the egg cups bake evenly. Lightly coat a 12-slot muffin tin with nonstick spray, making sure to get the bottom and sides of each cup so the ham releases easily after baking.

Make the ham cups: Press 1 slice of deli ham into each muffin cup, gently shaping it so it lines the bottom and sides. It’s okay if the edges ruffle a little. That actually helps create the crispy, browned edges! Take 1 cup shredded cheddar cheese and sprinkle evenly among the ham cups.

Add the eggs: Crack 1 large egg into the center of each piece of ham.

Season the eggs: In a small bowl, stir together ⅛ tsp coarse salt, ⅛ tsp black pepper, ⅛ tsp onion powder, ⅛ tsp garlic powder, and ⅛ tsp red pepper flakes. Sprinkle the seasoning mixture evenly over the eggs for a extra flavor in every bite. You can omit the pepper flakes if you don’t like spice.

Bake: Bake for 12-15 minutes, depending on how you like your yolks. Pull them closer to 12 minutes for softer yolks, or bake a little longer for firmer centers. Either way, the whites should look set and opaque, and the ham edges should be lightly crisp.

Garnish: Remove the egg cups from the oven and sprinkle with fresh chopped parsley.

Serve your ham and cheese egg cups warm, and enjoy!

Serving Suggestions

Since these egg cups are so easy to make ahead, they’re great for meal prep and busy mornings when breakfast needs to come with you. A fresh fruit salad keeps things light and colorful, while banana muffins are another easy grab-and-go option if you’re packing breakfast for work or school. For weekends, I’d add toast and crispy hash browns and call it a cozy sit-down breakfast.

Storing Leftovers

• Fridge. Store leftover ham and cheese egg cups in an airtight container in the fridge for up to 3-4 days. You can enjoy them cold or reheated. Reheat in the microwave for about 30 seconds, or until heated through. Keep in mind the ham can become a bit chewier in the microwave. The eggs will also cook more as they reheat, so softer yolks will become a little firmer.
• Freezer. You can freeze these egg cups, but the eggs may turn rubbery and release some moisture after reheating. If that doesn’t bother you, freeze them in a single layer on a baking sheet for 1 hour. Then transfer to freezer-safe bags or containers for up to 2 months. Thaw before reheating when possible, or reheat straight from frozen.

More Grab-and-Go Egg Breakfast Recipes:

• It takes just 1 minute to whip up a fluffy, light, creamy, and crave-worthy Soufflé-Style Egg that tastes like it came out of a restaurant kitchen.
• Easy to make ahead, pack up, and reheat, these Egg Muffins are a quick breakfast that travels well.
• Just Crack An Egg is a hot microwave breakfast with eggs, potatoes, ham, cheese, and veggies.

I hope you love this delicious and easy recipe – be sure to give it a review below! Also don’t forget to follow Belly Full on TikTok, Instagram, Facebook, Pinterest, and YouTube!