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By Rachael | Updated on

Jalapeno Popper Egg Muffins:

With just 15 minutes of your time, you get this high protein breakfast option can be made ahead for a quick tasty meal that is low carb and keto friendly. These egg bites or egg muffins are eggs, cheese, bacon, and jalapeños to make a fun breakfast version of the classic appetizer jalapeños poppers.

Jalapeños poppers aren’t exactly known for being healthy, with the deep frying etc. But they sure taste good. The heat of the jalapeños mixed with the creaminess of the cream cheese and cheese and the saltiness of the bacon make them a classic for a reason. In this breakfast egg muffin, I am taking all the things we love about the flavors of the jalapeños popper, and making a healthy breakfast twist. And with very little prep.

jalapeno popper egg muffins stacked in a stack of three with a few slices of jalapenos around

I have always been more into savory foods than traditional sweet breakfast foods. Give me a bowl of taco soup over keto pancakes any day, I will eat the pancakes for lunch. But eggs, eggs are a different story. I love eating egg muffins or egg cups at breakfast. They are just the right amount of flavor, a great source of protein, and provide so many awesome benefits. Because I think I started making egg muffins for breakfasts, and freezing them. In the morning, I can pop one out of the freezer and microwave it for 30 seconds to a minute, and I get a hot, egg breakfast that is delicious!

I started with a basic ham and cheese egg muffin, as that is what I traditionally like in my omelettes. But then I tried buffalo chicken egg muffins, and it opened up my eyes to the world of possibilities with these egg cups. I could have the flavors of appetizers like buffalo wings and jalapeno poppers, for breakfast!

If you want to make these great meal prep breakfast ideas, then here is what you need to know:

Egg Muffin Tips

  • Bake for 12-17 minutes until set. The reason the range is so long besides the fact that every oven acts differently, is eggs come in different sizes, and the distribution of the cheese and cream cheese can impact cooking times. The idea is to cook them through without overcooking, so give the tray a gentle shake and if the middle isn’t too jiggly, the egg cup is good to go.
  • Add your toppings mixed in, but also add some at the top to make it look pretty. We eat with our eyes before we eat with our mouthes which means you want your breakfast to look appealing. You can accomplish this by adding a little sprinkle of cheese and slice of jalapeno to the top of your egg cup before baking.
  • Spray your muffin tin with non-stick cooking spray or use a silicone baking mold to make sure the eggs do not stick to the pan and you can get your muffins out.

Jalapeno popper egg cups in a silicone baking tin

Will the eggs stick to cupcake liners?

Breakfast Egg Muffins / Cups might be the perfect make-ahead protein-packed low carb keto breakfast, but if they stick to the pan and you can’t get them out they won’t do you any good. Plus, you don’t want them falling apart on you. The best solution is to make sure to spray your pan with cooking spray before you add the eggs to it. This will help prevent them from sticking.

Another great solution, which you can see I employed above is to bake your egg muffins in a silicone baking mold instead of a traditional muffin tin. I love this silicone baking mold I grabbed off Amazon as nothing sticks to it, and it is very easy to clean. You can find it here. You can also find different size muffin “tins” that come in silicone, so you can make baby bites for kids, or larger egg muffins if you want to add something like sausage patties to the bottom part.

Jalapeno popper egg muffins stacked on a wooden cutting board

Reheating Egg Muffins

Once you have cooked your egg muffins you can eat them right away for breakfast (lunch or dinner too) or you can freeze them and save them for later. If you do this, you will want to reheat them in a way that does not overcook them. I read a lot about whether or not it is safe to reheat eggs, and it seems like there is information going both ways. However, according to the FDA you can serve cooked eggs and egg-containing foods (such as such as quiches and soufflés) immediately after cooking, or you can refrigerate them for later but they need to be thoroughly reheated to 165 degrees F before you serve them.

Another concern people have is eggs becoming rubbery if you reheat them. I can admit this has happened to me a time or two. The trick is not cooking them too long. Rubbery is a sure sign of over-cooked. So here are a few tips for reheating egg muffins in various ways so they are just as good as freshly made.

Can you Reheat Eggs in the Microwave?

Eggs are so versatile and fun, but even though they cook quickly, it seems like a hassle on busy mornings, and can result in too many dishes. But the good news is your microwave can be used to reheat these jalapeno popper egg cups so you do not have to make them fresh. In fact these eggs muffins were specifically designed to be cooked ahead of time, then microwaved so they can be enjoyed on the go. You can two options:

  1. Put eggs in the fridge the night before so they defrost, then merely microwave 30 seconds to reheat.
  2. Remove eggs from freezer and microwave for 1 minute with a little cup of water in the microwave as well. This will act like a steamer and keep you from overcooking while the egg defrosts.

One thing to keep in mind is the cheese mixed in with the eggs at original cook time can help to keep them from getting too tough when you reheat. So be liberal and generous with the cheese.

If you have the time, a great way to reheat eggs is steaming them. These egg muffins can be steamed for just 30-40 seconds and turn out awesome!

six jalapeno popper egg muffins on a cutting board with some sliced jalapenos

How Long Do Cooked Eggs Last?

These egg muffins can last a couple months if frozen, and 4-6 days in the refrigerator if not.

Hard-boiled eggs last about a week refrigerated, but eggs cooked other ways have a shorter shelf life, and should be stored at 40 degrees F or less in the refrigerator so bacteria can’t grow on them.

If you’re a fan of jalapeno poppers, then do yourself a favor and give these a try, they only take 15-20 minutes of your time, are low prep, and full of flavor.

Other Fun Egg Cup Flavors

  • Broccoli Cheese Breakfast Egg Muffins
  • Buffalo Chicken Breakfast Egg Muffins
  • Sausage, Spinach, Ham and Egg Cups
  • Sun-Dried Tomato, Spinach and Cheese Egg Cups

jalapeno popper egg muffins stacked in a stack of three with a few slices of jalapenos around

Jalapeño Popper Breakfast Egg Muffins

Jalapeno Popper Egg Muffins: with just 15 minutes of your time, you get this high protein breakfast option can be made ahead for a quick tasty meal that is low carb and keto friendly. These egg bites or egg muffins are eggs, cheese, bacon, and jalapeños to make a fun breakfast version of the classic appetizer jalapeños poppers.


Course: Breakfast

Cuisine: American

Keyword: egg, egg cup, egg muffin, egg muffins, keto, low carb

Prep Time: 7 minutes

Cook Time: 15 minutes

Total Time: 22 minutes

Servings: 12 egg muffins

Calories: 98kcal


  • 10 large eggs
  • 1 teaspoons sea salt or to taste
  • 1/4 teaspoon black pepper or to taste
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 3-4 jalapeño peppers de-seeded and chopped
  • 1/3 cup cream cheese softened
  • 1/2 cup cheddar cheese shredded
  • 1/3 cup bacon cooked crumbled


  • Preheat oven to 400 F.

  • Get a 12 count muffin tin, and line with silicone liners, or use a silicone muffin pan. Or coat a regular muffin pan with non-stick cooking spray. Set aside.

  • In a large mixing bowl, crack in eggs and whisk together with salt and black pepper.

  • Add in all other ingredients

  • Divide evenly into muffin tins filling each about 2/3 full. Top with cheese.

  • Place 1-2 jalapeño slices on top in each muffin cup.

  • Bake in preheated oven for 12-17 minutes, or until set.


Calories: 98kcal | Carbohydrates: 1g | Protein: 6g | Fat: 7g | Saturated Fat: 3g | Cholesterol: 148mg | Sodium: 300mg | Potassium: 75mg | Vitamin A: 365IU | Vitamin C: 5mg | Calcium: 61mg | Iron: 0.7mg

Our recipe card software calculates these nutrition facts based on averages for the above ingredients, different brands, and quality of produce/meats may have different nutritional information, always calculate your own based on the specific products you use in order to achieve accurate macros for this recipe.

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Jalapeno popper egg muffins in a stack


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