Low-Carb Pesto Egg Breakfast Cups with Bacon

These muffin cups are so full of flavor and easy to make.  Plus, you can make a whole batch of these and freeze to make for easy, grab-and-go breakfasts on those busy mornings.  Because these egg cups freeze so well, I like to make them earlier in the week.  I just take out the desired number we need the night before we have an early check for a sporting event, and breakfast is ready to go after a quick reheat. 

These low-carb egg cups have become a staple in our household, especially for busy weekends.   These are naturally grain-free and gluten-free, but you can easily customize them to your liking.  These egg cups are such an easy way to get protein into your diet.  They make for the perfect protein-packed breakfast or afternoon snack!

pesto egg bites
pesto egg cups ingredients

Simple Ingredients

  • Dairy-free milk – You can use any dairy-free (or regular) milk you prefer.  Just be sure that you are using unsweetened and unflavored milk.  Recently, I have been using a lot of cashew milk in my recipes as it is extra creamy, but almond, coconut, or any other unsweetened, unflavored variety will work!
  • Pesto – You can use any pesto that you like.  My favorite dairy-free pesto is made by Gotham Greens.  Note: Most store-bought pesto contains dairy.   Be sure to read the label carefully, if you have a dairy sensitivity or allergy.
  • Lemon juice – I think this enhances the savory flavors of this dish and counterbalances any subtle sweetness from the unsweetened nut milk.  If you don’t have this on hand, you can omit it.
  • Salt and pepper – Just a little bit of both of these ingredients goes a long way and naturally enhances and highlights the flavors of this dish.
  • Bell pepper – Just be sure to dice your bell peppers to a small size so they cook through.  You can substitute for cherry tomatoes.  Just cut into tomato halves or quarters.  Because tomatoes can we watery, be sure to leave any excess water from the tomatoes on the cutting board. 
  • Bacon – As a matter of preference, I used bacon for this recipe.  However, for a fancier occasion, prosciutto makes an excellent substitute.  If you are wanting to make ham cups, you will need 12 ham slices.  Place one ham slice in each muffin cup, pour the egg mixture in, and cook as outlined below.  The edges of ham get nice and crispy, making these delicious ham-lined muffin cups.
  • Green onions – For that uniquely, subtle onion flavor, green onions work best in this recipe.
  • Manchego cheese – If you are dairy-sensitive or allergic, you can omit this completely or use your favorite dairy-free cheese.  Although I have some sensitivities to cow’s dairy, I can tolerate goat and sheep’s milk in small amounts.  Manchego cheese reminds me of cheddar cheese, so that is my personal preference.  Goat cheese and feta (sheep or goat) make great substitutions too.  For a Mediterranean spread, one teaspoon feta cheese in each of the egg bites makes for the perfect feta muffin bites.
  • Other Additions – I intentionally made these low-carb.  However, if that is not a concern to you, cubed and toasted grain-free or gluten-free bread, diced and cooked sweet potatoes or hashbrowns make excellent additions to these egg cups.  

Prepare Muffin Tins

There are a variety of methods that can be used to prepare muffin tins.  You can certainly use silicone muffin tins.  I try to steer clear of silicone when heat is involved to prevent any leaching from the plastic.  If you are going the cooking spray route, be sure to generously spray your muffin tin so the egg muffins pop right out when they have cooled.  My preferred method is to use muffin liners or parchment liners.  This helps the muffins pop right out of the muffin pan and prevents them from sticking together when storing the freezer.  See cooling tips below on why this is important.

Regular Size Muffins vs Mini Muffins

There is just something so adorable about mini muffins.  This recipe makes for the perfect one-bite savory offering at a baby or wedding shower or ladies’ lunch.  To make these in a mini version, just use a 24-serving mini-muffin pan instead, being sure to follow one of the methods above to prevent sticking.  These will cook much faster, so I would check for doneness beginning at 12 minutes.


It is recommended that you cool on a wire rack for several reasons:

  • Prevents overcooking – To prevent overcooking, remove parchment-lined egg muffins from the hot muffin tin and cool a wire rack.  The air circulation will help stop the cooking process.
  • Allow moisture to escape – If egg muffins are left in hot muffin tins or placed on a counter instead of a wire rack, the bottoms of the egg muffins can get soggy as moisture accumulates. 


Be sure to allow your egg muffins to cool completely on a wire rack before storing them.  Storing hot or even warm muffins can create condensation, leaving to soggy muffins.  

  • Refrigerator: Put cooled egg muffins in an airtight container and store in the refrigerator.   Placing a towel in the bottom of the container will help absorb any excess moisture.  These egg muffins will keep in the refrigerator for 4-5 days.
  • Freezer:  After cooling completely, individually wrap in parchment paper to prevent muffins from sticking.  Add to freezer Ziplock.  When ready to serve, put in the refrigerator the night before serving.  Reheat in air fryer, oven or microwave.  You can freeze the egg muffins for 2-3 months.
pesto egg bites

Low-Carb Pesto Egg Breakfast Muffin with Bacon

Sarah Erickson
This is an easy recipe to meal prep for days when you need a grab-and-go breakfast!
Prep Time 5 minutes
Cook Time 20 minutes
Course Breakfast
Cuisine American


  • 10 eggs
  • 1/4 cup unsweetened dairy-free milk
  • 1/4 cup pesto plus more as desired
  • 1/4 teaspoons lemon juice
  • 1/2 teaspoon salt
  • 1/2 teaspoon pepper
  • 1/2 cup bell pepper finely diced
  • 6 slices bacon cooked and crumbled
  • 4 green onions thinly sliced
  • 1 cup shredded Manchego


  • Preheat oven to 375 degrees F.
  • Line muffin tins with parchment cups.
  • In a large bowl, mix together the eggs, milk, pesto, lemon juice, salt and pepper.
  • Evenly distribute the remaining ingredients (bell pepper, bacon, green onions, cheese) in each of the muffin cups.
  • Evenly divide the egg and pesto mixture between each of the 2-inch muffin cups.
  • Bake for 20 minutes or until eggs are set.


12-hole muffin tin (or silicone)
Cooking spray or muffin liners
Keyword breakfast, dairy free, eggs, gluten free, low carb

Similar Posts

Leave a Reply