Gluten Free Meal Prep Scramble Cups (Low Carb)

Make your busy weekday mornings a bit easier with these Gluten Free Meal Prep Scrambled Egg Cups (aka microwave omelets). Just spend a few minutes ahead of time prepping veggies to set up 3-4 days of gluten free, dairy free, and low carb breakfasts.
Gluten free, low carb, dairy free if using non-dairy cheese
Course Breakfast
Cuisine American
Keyword microwave eggs, scrambled egg cups, scrambled eggs microwave
Prep Time 10 minutes
Cook Time 2 minutes
cooling time 3 minutes
Total Time 12 minutes
Servings 3 servings
Calories 229kcal
Author Sarah Jane Parker


  • 6 Tablespoons red bell pepper, diced
  • 6 Tablespoons yellow or orange bell pepper, diced
  • 6 Tablespoons bacon crumbles
  • 6 Tablespoons dairy free shredded cheese (or real cheese if tolerated)
  • 6 eggs
  • 3 Tablespoons finely sliced green onion or chives
  • Glass meal prep bowls
  • Smoked salt (or regular salt)
  • Black pepper
  • Tabasco, harissa, or other favorite sauce for topping (optional)


For meal prep scramble cups:

  • Divide your diced bell peppers, green onions, and bacon or sausage crumbles into the meal prep cups.  
  • Put the lids on the cups and store in the fridge for up to 4 days. 

Cooking your scrambled egg cups:

  • Crack 2 eggs into the cup of prepped veggies and add dairy free or regular cheese and seasonings as you like, stir it up, then heat in the microwave for 50 seconds. If you want to add 3 eggs, you'll need to increase the time slightly and add another cooking segment.
  • Take the scrambled egg cup out of the microwave, then stir it and mix it well again (it will be cooked on the outside but not in the middle at this point).
  • Return it to the microwave for another 30 seconds. This is usually sufficient, but stir again and heat again for 20 seconds if it's still soft on top. If using 3 eggs, you'll need to stir again and add another 30 second cooking time. 
  • Be careful removing this out of the microwave, it will be pretty hot!
  • Allow to cool for a few minutes before eating. You can top your scrambled egg cup with your more green onion, avocado slices, harissa, Tabasco, or anything you like!



Calories: 229kcal | Carbohydrates: 6g | Protein: 17g | Fat: 14g | Saturated Fat: 5g | Polyunsaturated Fat: 0g | Monounsaturated Fat: 0g | Trans Fat: 0g | Cholesterol: 347mg | Sodium: 671mg | Potassium: 216mg | Fiber: 1g | Sugar: 2g | Vitamin A: 1700IU | Vitamin C: 48.6mg | Calcium: 54mg | Iron: 1.8mg