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Breakfast Egg Muffins with Meal Prep Instructions

Easy, low carb, and freezer friendly Keto Breakfast Egg Muffins are a perfect make ahead healthy breakfast for people on the go. Add any veggies you like, mix with eggs and cheese, then bake!


Breakfast Egg Muffins are an amazing Keto Breakfast recipe packed with flavor and healthy ingredients. Egg Muffins come together relatively quick and can easily be customized with your favorite add ins.

My favorite part is that they keep well in the fridge for days, and can also be frozen! 🙌 We make these easy egg muffins ahead of time and reheat them throughout the week for a perfect meal on-the-go.

When I snooze the alarm more than 3 times, nothing saves the day (or morning) like these guys. Honest. I throw them in the microwave for about 40 seconds and pass them around while driving everyone to their destination. 

Egg Muffin Cups

How to Make Breakfast Egg Muffins

  • First, you want to choose what you would like to include inside the egg muffins. My choices are always the following three, and I make all three in a 12-cup muffin tin. 

Ingredients for Breakfast Egg Muffins

  1. Feta, spinach, tomatoes, and red onions.
  2. White cheddar, sliced mushrooms, and diced sun-dried tomatoes in oil.
  3. Sharp cheddar, BACON, and broccoli.

There’s a 4th choice, here, too. It includes all of my leftovers. YES, leftover meats and veggies from the week. Throw them in there and you’ll look forward to making more leftovers. 

  • Next, after dicing up and prepping our mix-ins, grab your eggs and crack them open. 
  • Add the eggs to a mixing bowl with your favorite seasonings and whisk them well. 
  • Generously spray a muffin tin with cooking spray. 
  • Arrange your add-ins – veggies, cheeses, and meats – inside the muffin cups.
  • Divide the egg mixture evenly among muffin cups, only about 2/3 full, and bake. Don’t fill the muffin cups to the top — the eggs will overflow and make a big mess in the oven. 
  • Bake at 400F for 12 to 15 minutes, or until eggs are set. 

A make ahead, simple breakfast, ideal for those of you that are always on the go. It’s a high protein, low carb, Keto breakfast recipe, and a wonderfully delicious treat.

Breakfast Egg Muffins


To start, you will need to get some meal prep containers. My favorites (affiliate link)  ⬇️

Meal Prep Containers

Next, you want to decide what you would like to prepare for your breakfast meal prep.

My suggestions are cheese (ALWAYS!), almonds, berries, and two egg muffins. You get your protein, your veggies, fruits, and nuts! That’s a pretty nice, well balanced meal. 

Keep in the fridge until ready to eat/serve. Reheat muffins before serving.

Breakfast Meal Prep with Egg Muffins


Store completely cooled egg muffins in a ziploc bag. Keep in the fridge for up to 5 days.


Store completely cooled egg muffins in a ziploc bag. Keep in the freezer for up to 3 months. 

Breakfast Egg Muffins - Keto Breakfast Recipe



Easy Breakfast Egg Muffins | Tasty & Healthy Keto Breakfast Idea

Breakfast Egg Muffins

Katerina | Diethood
Easy, low carb, and freezer friendly Keto Breakfast Egg Muffins are a perfect make ahead healthy breakfast for people on the go. 
4.89 from 9 votes
Servings : 12
Prep Time 10 minutes
Cook Time 15 minutes
Resting Time 5 minutes
Total Time 25 minutes


  • 10 large eggs
  • 1 teaspoon salt, or to taste
  • 1/4 teaspoon fresh ground black pepper, or to taste
  • 1/3 cup chopped baby spinach
  • 4 tablespoons crumbled feta cheese
  • 4 cherry tomatoes
  • 2 tablespoons chopped red onions
  • garlic powder, to taste
  • dried basil, to taste
  • 4 button mushrooms, sliced
  • 4 tablespoons diced sun dried tomatoes in oil
  • 4 tablespoons shredded white cheddar cheese
  • Italian Seasoning, to taste
  • 4 tablespoons cooked, chopped bacon
  • 4 tablespoons shredded cheddar cheese
  • 1/3 cup broccoli florets, chopped
  • garlic powder, to taste


  • Preheat oven to 400F.
  • Generously spray a 12-cup muffin tin with cooking spray. Set aside.
  • Crack the eggs into a large mixing bowl; season with salt and pepper, and whisk until well combined. Set aside.
  • Divide each of the three add-in combinations into 4 muffin cups.
    That is: 4 muffin cups to be filled with the Feta and Spinach Mixture; 4 muffin cups to be filled with the Mushrooms and Sun-Dried Tomatoes Mixture; 4 muffins cups to be filled with the Bacon, Cheddar, and Broccoli Mixture.
  • Pour the previously prepared egg mixture over the toppings, coming up about half-way to 2/3 full. DO NOT fill muffin cups to the top - the eggs will overflow.
  • Bake for 13 to 15 minutes, or until eggs are set.
  • Remove from oven and let cool for 5 minutes.
  • Run a butter knife around the edges of each muffin to loosen it.
  • Remove egg muffins from the pan and serve.
  • If using later, let egg muffins cool on a wire rack and refrigerate or freeze. See recipe notes.


  • Feel free to swap the listed ingredients for the same amount of any other vegetable, cheese, or cooked, diced meat.
  • Store completely cooled egg muffins in a ziploc bag. Keep in the fridge for up to 5 days.
  • Store completely cooled egg muffins in a ziploc bag. Keep in the freezer for up to 3 months.


Serving: 1 Egg Muffin | Calories: 122 kcal | Carbohydrates: 2 g | Protein: 9 g | Fat: 8 g | Saturated Fat: 3 g | Cholesterol: 153 mg | Sodium: 377 mg | Potassium: 193 mg | Fiber: 0 g | Sugar: 0 g | Vitamin A: 485 IU | Vitamin C: 9.1 mg | Calcium: 108 mg | Iron: 1 mg | Net Carbs: 2 g

Nutritional info is an estimate and provided as courtesy. Values may vary according to the ingredients and tools used. Please use your preferred nutritional calculator for more detailed info.

Course: Breakfast, Breakfast/Brunch, Breakfast/Snacks
Cuisine: American/Southern, Mediterranean
Keyword: breakfast muffins, egg muffins, keto breakfast ideas, keto recipes, low carb recipe
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15 comments on “Breakfast Egg Muffins with Meal Prep Instructions”

  1. Hi, something went wrong with mine. They are dry but the flavor is good. I froze them and popped one in the mic this morning for 35 seconds, then 5 seconds more because the middle wasn’t done. I should have tried one before I froze them because now I’m not sure if it was the original cooking process or the freezing and reheating. Per the recipe, I baked them at 400 for 13 minutes. Cooled for 5 them removed from tins and cooled on racks completely before freezing. The looked good, browned on the bottom. What do you think?

    1. Avatar photo
      Nancy Williams

      When reheating anything…eggs, cooked chicken, etc….use the defrost setting on your microwave. It reheats but does not cook on high and therefore does not over-cook and toughen the product you are trying to just reheat. Try adding a few drops of water to the product as well. Microwaves use moisture to cook or reheat. This is how I always reheat food.

  2. Avatar photo
    Erin | Dinners,Dishes and Dessert

    These sound delicious! Dangerously good… These would disappear in our house!

  3. Avatar photo
    Jade Manning

    I love these, perfect get up and go for any busy mornings, I pre-made these night before were so good!!

  4. Avatar photo
    Chrissie Baker

    Breakfast Egg Muffins is a wonderful idea. Made them this morning for the week. Endless combinations of ingredients for future batches. THANK YOU

  5. Oh, I love these egg muffins. My daughter feels bored at my breakfast these days. I think I can try this recipe. And my daughter will love these egg muffins. Hope I can do the same as you.

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