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tomato basil egg muffin cups.
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5 from 88 votes

Tomato-Basil Egg Muffin Cups

Easy Egg Muffin Cups are mini omelets made in a muffin tin. Perfect for a grab-and-go breakfast or to freeze ahead for a protein-packed start to the day with no effort.
Prep Time10 minutes
Cook Time25 minutes
Total Time35 minutes
Course: Breakfast
Cuisine: American
Diet: Gluten Free, Low Calorie, Low Fat
Servings: 6 2 mini omelets per serving
Calories: 140kcal
Author: Toni Dash


  • 10 large eggs
  • ¼ cup non-fat milk low fat milk can also be used
  • teaspoon black pepper
  • ¼ teaspoon kosher salt
  • ½ cup diced cherry tomatoes
  • cup diced fresh basil
  • cup diced yellow onion
  • cup shredded reduced-fat cheddar cheese


  • 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.
  • In a 4 cup glass measuring cup or mixing bowl, whisk together the eggs and milk. Add the pepper and salt; whisk in.
  • Add the tomatoes, basil, onion and cheese; stir to combine. Evenly distribute in the prepared muffin tin (will fill to just below to the top of each cavity).
  • 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).


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.
To change up these egg muffins:
  1. Use the same amount of eggs and milk as in the recipe
  2. 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.
  3. Use ⅓ cup shredded cheese or swap in a different filling ingredient for the cheese.


Calories: 140kcal | Carbohydrates: 3g | Protein: 13g | Fat: 8g | Saturated Fat: 3g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 3g | Trans Fat: 1g | Cholesterol: 312mg | Sodium: 260mg | Potassium: 181mg | Fiber: 1g | Sugar: 2g | Vitamin A: 615IU | Vitamin C: 4mg | Calcium: 92mg | Iron: 2mg