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Broccoli Cheddar Cups are a kid-friendly breakfast, lunch or snack idea that the whole family will love. Broccoli, bell peppers and onions are mixed together with eggs and cheddar cheese and baked into delicious egg muffins packed with calcium and protein. The perfect start to your day or an easy packable lunch or snack.
These broccoli cheddar egg muffins take about 40 minutes start to finish and bake up light, fluffy, and packed with 8 grams of protein each. Broccoli, sweet onion, and bell pepper get sautéed until tender, then folded into whisked eggs, egg whites, and sharp cheddar with a pinch of warm nutmeg. The result is a muffin that holds together well, reheats in under a minute, and doesn’t turn rubbery or watery like a lot of egg muffin recipes do.
I make a batch of these most Sunday nights so my husband has a grab and go breakfast for the car, and so the kids have an easy protein packed option for school mornings or lunchboxes. They freeze well too, which makes this one of the easiest meal prep wins in my breakfast rotation. If you like egg muffins try these Caprese Egg Muffins, Pizza Egg Muffins, or these Breakfast Egg Muffins.
Why This Recipe Works
Sautéing the onion and bell pepper before mixing removes excess moisture, which is the main reason egg muffins turn watery or fall apart. Steaming the broccoli separately keeps its texture intact instead of releasing water directly into the egg base.
Using a mix of whole eggs and egg whites keeps the muffins light and higher in protein without making them dense. A small amount of nutmeg rounds out the sharpness of the cheddar and gives the eggs a subtle warmth, a small technique borrowed from how warm spices are traditionally used in Mediterranean egg dishes to deepen flavor without overpowering it.
Recipe Ingredients
For exact ingredient amounts and instructions, see the full recipe card below.
- Broccoli. Steam it just until tender before adding it to the eggs. Overcooked broccoli releases extra water and can make the muffins soggy.
- Eggs and egg whites. The combination keeps these muffins light and higher in protein than a full whole egg version, without making them taste eggy or overly dense.
- Sweet onion. Adds mild sweetness once sautéed. A yellow onion works too if that’s what you have on hand.
- Bell pepper. Any color works well here. Red or orange will give a slightly sweeter flavor than green.
- Cheddar cheese. Sharp cheddar gives the best flavor payoff, but a mild or medium cheddar works fine for a gentler taste, especially for younger kids.
- Nutmeg. A small amount rounds out the sharpness of the cheddar and adds warmth to the eggs. Don’t skip it, it makes a noticeable difference for such a small amount.
Modifications
- Spinach Feta: Swap the broccoli for chopped spinach and use crumbled feta instead of cheddar for a lighter, tangier version.
- Lebanese Za’atar Style: Stir a teaspoon of za’atar into the egg mixture in place of the nutmeg for a warm, herby flavor that pairs beautifully with the sharp cheddar.
- Southwest Style: Swap the bell pepper for diced jalapeño and top with pepper jack instead of cheddar for a spicier, smokier version.
- Mushroom and Swiss: Add a handful of chopped sautéed mushrooms along with the broccoli and swap the cheddar for Swiss for an earthier flavor.
- Ham and Cheddar: Fold in 1/2 cup of finely diced cooked ham for a heartier, protein boosted muffin that’s great for a bigger breakfast.
- Sun-Dried Tomato and Aleppo Pepper: Stir in chopped sun-dried tomatoes and a pinch of Aleppo pepper instead of nutmeg for a smoky, slightly sweet Mediterranean twist.
How to Make these Egg Muffins
Step 1: Prepare Muffin Tin: Preheat the oven to 375 degrees. Grease your muffin tins {enough for 14-16 large muffins} and set aside.
Step 2: Cook Broccoli: Steam or cook the broccoli florets until tender. Remove from heat and set aside.
Step 3: Whisk Eggs: In a large bowl, crack the eggs and add the egg whites. Whisk together and set aside.
Step 4: Saute Vegetables: In a large skillet heat 2 Tablespoons olive oil over medium high heat. Add the onion and bell pepper and sauté for 6-7 minutes, until the onion is soft.
Step 5: Add the Vegetables with the Eggs: Add the cooked vegetables and broccoli to the eggs along with 1 cup of the cheddar cheese. Mix to combine. Add the nutmeg, salt and pepper and gently stir to combine everything together.
Step 6: Add Eggs to Muffin Tins: Pour the egg mixture into the greased muffin tins {about 3/4 of the way full} and sprinkle each muffin with a small amount of the 1/2 cup of cheddar cheese.
Step 7: Bake: Put the egg muffins in the oven and bake for 20-25 minutes until the egg muffins are set in the middle and begin to turn golden brown on the edges.
Remove from the oven and let cool for about 10 to 15 minutes before removing from the muffin tin. Refrigerate the egg muffins in an airtight container for up to 4 days.
Common Mistakes to Avoid
- Skipping the sauté step. Raw onion and pepper release water as they bake, which leads to soggy muffins.
- Overfilling the muffin cups. Fill only about three quarters full since the eggs puff up significantly while baking.
- Under greasing the tin. Egg muffins stick easily. Grease the sides and bottom of every cup generously, even with a nonstick pan.
- Overbaking. Pull the muffins as soon as the centers are set and the edges are just golden. A few extra minutes will make them rubbery.
- Skipping the cooling time. Letting the muffins rest for a few minutes in the tin before removing helps them hold together instead of falling apart.
Storage Instructions
- Store the egg muffins in an airtight container in the refrigerator for up to 4 days. Reheat in the microwave for 20 to 30 seconds, or until warmed through.
- To freeze, let the muffins cool completely, then wrap each one individually and store in a freezer safe container or bag for up to 3 months. Reheat from frozen in the microwave for 1 to 2 minutes.
More Egg Recipes
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Broccoli Cheddar Cups
Ingredients
- 3 cups broccoli florets, steamed
- 2 tablespoons olive oil
- 8 eggs
- 4 egg whites
- 1/2 cup sweet onion, chopped
- 1/2 bell pepper , {color of your choice} seeds removed, chopped
- 1 1/2 cups cheddar cheese, separated
- 1/4 teaspoon nutmeg
- 1/8 teaspoon salt
- 1/8 teaspoon pepper
Instructions
- Preheat the oven to 375 degrees. Grease your muffin tins {enough for 14-16 large muffins} and set aside.
- Steam or cook the broccoli florets until tender. Remove from heat and set aside.
- In a large bowl, crack the eggs and add the egg whites. Whisk together and set aside.
- In a large skillet heat 2 Tablespoons olive oil over medium high heat. Add the onion and bell pepper and sauté for 6-7 minutes, until the onion is soft.
- Add the cooked vegetables and broccoli to the eggs along with 1 cup of the cheddar cheese. Mix to combine. Add the nutmeg, salt and pepper and gently stir to combine everything together.
- Pour the egg mixture into the greased muffin tins {about 3/4 of the way full} and sprinkle each muffin with a small amount of the 1/2 cup of cheddar cheese.
- Put the egg muffins in the oven and bake for 20-25 minutes until the egg muffins are set in the middle and begin to turn golden brown on the edges.
- Remove from the oven and let cool for about 10 to 15 minutes before removing from the muffin tin. Refrigerate the egg muffins in an airtight container for up to 4 days.
Notes
- Grease the muffin tin generously, including the sides, since eggs stick easily even in a nonstick pan.
- Sauté the onion and bell pepper before mixing. This step removes excess moisture and is the main reason these muffins don’t turn watery like a lot of egg muffin recipes.
- If using frozen broccoli, thaw it fully and pat it dry before adding it to the mix.
- Pull the muffins as soon as the centers are set and the edges turn golden. A few extra minutes in the oven will make them rubbery.
- To freeze, wrap each muffin individually in plastic wrap and store in a freezer safe bag for up to 3 months. Reheat from frozen in the microwave for 1 to 2 minutes, until warmed through.
- For a Mediterranean twist, swap the nutmeg for a teaspoon of za’atar.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Today’s recipe is sponsored by ADA Mideast. As always, my opinions are 100% my own.
Such a great breakfast for kids
These were easy to make and delicious. I good alternative to cereal. Can you give the nutrition amounts?
Julia: Question: say you dont have brocolli–does zucchin have too much mosture if you cook it first.
I was trying to think waht other green vegie one could substitute! Thanks for posting…..
Great question! I think zucchini works depending on how you add it in. One thought would be to dice it up and another thought would be to try shredding it and then using two paper towels to squeeze out the excess water. I honestly don’t know how it would turn out but I think it sounds good and would be worth a try. Other options would be spinach or kale, any type of bell pepper {sauté them first}. With any vegetable, I would quickly sauté them a little so they soften before adding them to the egg mixture to bake. Let me know what you end up doing and how you like them!