Tomato-Basil Cheese Egg Muffin Cups are a protein-packed start to the day! Mini omelets, muffin tin omelets, egg muffins or egg muffin cups; no matter what you call them these little omelets made in a muffin pan are a perfect start to busy mornings. These mini frittatas are so easy to change up with your favorite ingredients!
If you love an omelet but never have time to make one, this low-carb breakfast recipe is a great option to solve that craving. Healthy egg muffin cups are a great way to have an easy breakfast idea on the ready any time. Perfect for meal prep and they can go from freezer to microwave too.
They are often called egg muffins because they are made in a muffin pan (here is no flour in these easy egg muffins). This simple recipe is a perfect grab and go. Add this egg muffin cup recipe to your quick breakfast choices and healthy breakfast recipes list!
What makes this skinny?
This egg muffin cups recipe is delicious on it's own and you can customize it for your needs and favorite ingredients.
- Baking these allows no excess fat is needed to cook them
- Eggs are a great source of protein and a 2 egg muffins serving provides 13 grams of protein. Starting the day with protein keeps you full longer!
- Using filling ingredients of vegetables gives a wonderful flavor with great nutrition and low calories
- We used non-fat milk instead of a higher fat milk
- Reduced fat cheddar cheese gives the breakfast egg muffin cups some cheesy flavor without breaking the calorie bank.
Recipe Ingredient Notes
Eggs. Use 10 large fresh eggs.
Non-fat milk. We used non-fat milk for calorie savings. You can use any fat content dairy milk.
Cherry tomatoes. Cherry tomatoes or grape tomatoes can be used. Rinse, pat dry and slice or chop into small pieces. If you prefer larger tomato pieces slice as shown in the photos. Smaller pieces mix in more with the eggs; chop them for this. If substituting for a larger tomato use a roma tomato which is not as watery.
Fresh basil. Using fresh basil gives a wonderful fresh herb flavor to the little crustless quiche breakfast muffins.
Onion. Chop or dice the onion so it blends well with the egg mixture.
Reduced fat cheddar cheese. We use reduced fat cheddar cheese for calorie savings. Any shredded cheese can be used even fat-free. Adjust nutritional info accordingly.
How to make Egg Muffin Cups
STEP 1. Preparation
Preheat oven to 350 degrees. Spray a 12-cavity muffin tin (or 2 6-cavity muffin tins) with non-stick cooking spray and place on a rimmed baking sheet.
STEP 2. Create the egg muffin mixture
In a 4 cup glass measuring cup (this makes it easy to pour into the muffin pan) or mixing bowl, whisk together the eggs and milk (photos 1-2). Add the pepper and salt; whisk in (photos 3-4).
Add the tomatoes, basil, onion and cheese (photos 5-7); stir in to the beaten eggs to combine. Evenly distribute in the prepared muffin tin (will fill to just below to the top of each cavity) (photo 8).
STEP 3. Bake
Bake for 20-25 minutes until set (will rise and be puffy on top). Remove and allow to cool slightly (normal for them to deflate) (photo 9).
How to customize these Muffin Tin Eggs
All you need to do to make this egg muffins recipe your own is to follow this formula:
- Use the same amount of eggs and milk as in the recipe
- Substitute different ingredients for the vegetables or add meat: ½ cup + ⅓ cup + ⅓ cup. The total amount of ingredients is slightly over 1 cup.
- Use ⅓ cup shredded cheese or swap in a different filling ingredient for the cheese.
Using egg whites. You can cut back on some of the full eggs and substitute the equivalent volume of egg whites to further reduce the calories.
- Use your favorite veggies: red bell peppers, green bell pepper, green onions, spinach, leftover cooked broccoli.
- Seasoning ideas: onion powder, garlic powder, Italian seasoning, red pepper flakes or hot sauce for some spicy heat.
- Lean meat: diced ham, turkey, chicken, cooked ground turkey breakfast sausage or even a bit of crispy bacon.
- Cheese: you can leave the cheese out all together or try reduced fat feta cheese, goat cheese or other reduced fat shredded cheese. Regular fat cheese works too but has more calories.
How to Store
Store cooled egg muffins in an airtight container in the refrigerator for up to 3 days.
How to Freeze
It's easy to freeze these egg cups for a make ahead breakfast! Freezing them is a great time saver.
- Line a rimmed baking sheet with wax paper or parchment paper.
- Place fully cooled egg muffin cups on the prepared baking sheet with space in between.
- Place into the freezer and allow them to fully freeze.
- When frozen, place in a large freezer bag or freezer-proof airtight container. Place back in the freezer until use.
Note: because they were individually frozen first, they should not stick together and can be removed individually when desired.
How to Reheat
Every microwave cooks slightly differently so monitor to ensure the eggs are cooked through and not over cooked. Adjust times as needed for your microwave.
Chilled or thawed egg muffins: microwave for 30 seconds. Monitor the time as all microwaves cook differently.
Frozen: they can be reheated directly from the freezer too. This should take 1-2 minutes.
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