Smoked Salmon Egg Muffins

Full of smoked salmon, capers, and red onion, these Smoked Salmon Egg Muffins are just like your favorite bagel toppings… in a low-carb, high-protein breakfast option.  Easy enough for every day but fancy enough for brunch!

a six well muffin tin filled with smoked salmon egg muffins.

Last year, I shared these Southwestern Egg Muffins as one of our breakfast staples at the time.  Full of black beans, salsa, and other classic southwestern flavors, we’re still huge fans for quick and easy make-ahead breakfasts.

Now I’m updating the flavor to something a little more grown up… maybe.  Smoked salmon, red onion, and capers sounds more mature.  But in reality, I also made these smoked salmon egg muffins for my lox-obsessed two year old.

(It’s probably his favorite food.  Seriously.  On bagels, in egg muffins, in pasta salad, eaten plain – he likes it however he can get it.)

Just like the southwestern version, this is a breakfast I can totally get behind.  Full of protein and healthy fats, these are good for both little growing toddler brains and a delicious low-carb way for adults to start off their day, too!

egg muffin on a plate next to smoked salmon.

Ingredients and Substitutions

  • Eggs: For the best flavor, I recommend using fresh eggs, not eggs from a carton.
  • Milk: Use whatever milk or milk-like product you have. Whole milk, 2% milk, half-and-half, almond milk, soy milk – anything works.
  • Salt and Pepper
  • Herbs: I like to add a little parsley and chives (fresh or frozen works), but whatever herbs you like with salmon work well – dill would be a great addition, too!
  • Red Onion: Red onion has a better flavor for these muffins than yellow onions.
  • Capers: Capers provide the perfect briny flavor. Chopped green onions are a good substitute.
  • Smoked Salmon: The star of our smoked salmon muffins!
muffin wells filled with smoked salmon, capers, and red onion.

How to Make Smoked Salmon Egg Muffins

Making these muffins is a true piece of cake!

  1. Whisk together the eggs and milk. Stir in the herbs, salt, and pepper.
  2. Divide the red onion, capers, and smoked salmon between the 12 wells of the muffin tin.
  3. Pour the egg mixture into each cup. Stir with a fork to mix the eggs and the mix-ins.
  4. Bake until the egg muffins rise and set. Cool in the pan, then turn out and enjoy!

While the steps to make these is easy, what’s actually going on behind the scenes is a little more impressive. How do these egg muffins set and retain their shape? It’s time for my favorite subject – kitchen chemistry!

Kitchen Chemistry

Eggs can transform from a liquid state into a solid state when exposed to heat, thanks to albumin and globulin, proteins found in egg whites. These proteins are high in water but also capable of denaturing and coagulating when heated. As the temperature in the oven rises, the protein molecules in the egg whites begin to unfold, exposing new reactive sites and allowing them to bond with other proteins to form a network. This network of proteins is what gives structures to the muffins, trapping in the moisture and creating a light and fluffy egg muffin.

muffin tin filled with egg mixture to make egg muffins.

Perfect Make Ahead Brunch

The addition of smoked salmon makes these fancy enough to serve at brunch… without having to stand around flipping omelets one at a time for your guests.  Prep everything ahead of time, fill the muffin tins with the egg mixture, and store in the fridge until you’re ready to bake.

Make some waffles or pancakes or french toast, a fruit salad, and maybe a muffin or dessert pastry, and you have one deeee-licious brunch ready to go.  Don’t forget the mimosas!

two egg muffins on a plate filled with parsley and smoked salmon.
  • Mixing Bowls: These glass mixing bowls are my favorite – dishwasher and microwave-save, and all the sizes you need.
  • Whisk: A sturdy whisk makes mixing together the eggs and milk a snap.
  • Muffin Tins: Use light-colored muffin tins to prevent the outside of the muffins from getting too dark.
side view of an egg muffin with one forkful removed showing the smoked salmon on the inside.

Tips and Tricks for the Best Smoked Salmon Egg Muffins

  1. Pat the Smoked Salmon Dry: Before adding the smoked salmon to the muffin tins, pat it dry with a paper towel – excess moisture can affect the consistency of the muffins.
  2. Avoid Overmixing: Gently use a fork to stir together the egg mixture and the mix-ins. Overmixing the batter can result in tough or rubbery muffins.
  3. Customize with Herbs: Experiment with your favorite fresh or dried herbs, like dill, chives, or even everything bagel seasoning.
  4. Grease the Muffin Tins: Ensure the muffin tin is well-greased or use high-quality paper liners to prevent the muffins from sticking.
  5. Cool in the Tin: Let the muffins cool in the tin for a few minutes before attempting to remove them. This allows them to set and makes it easier to take them out without falling apart.
  6. Freeze for Later: If you have any leftovers, refrigerate or freeze them in an airtight container. These muffins can be enjoyed cold or gently reheated for a quick and convenient breakfast later.

More Breakfast Recipes

Smoked Salmon Egg Muffins: full of smoked salmon, capers, and red onion, these smoked salmon egg muffins are a delicious low carb, high protein breakfast option. {Bunsen Burner Bakery} #breakfast #brunch #eggs #smokedsalmon #glutenfree

Smoked Salmon Egg Muffins

Yield: 12 muffins
Prep Time: 5 minutes
Cook Time: 25 minutes
Total Time: 30 minutes

Full of smoked salmon, capers, and red onion, these smoked salmon egg muffins are just like your favorite bagel toppings… in a low carb, high protein breakfast option.


  • 12 large eggs
  • 1/2 cup milk
  • 2 teaspoons chopped parsley
  • 2 teaspoons chopped chives
  • salt and pepper, to taste
  • 1/4 cup red onion, diced
  • 1/4 cup capers
  • 3 ounces smoked salmon, sliced into half-inch strips


  1. Preheat the oven to 375 °F.  Spray a 12-well muffin tin well with cooking spray.
  2. In a large bowl, whisk together the eggs and milk until yolks are broken and well combined.  Stir in the parsley, chives, salt, and pepper.
  3. Divide the onions, capers, and smoked salmon among the 12 wells of the muffin tray.  Pour in the egg mixture into each cup, filling almost to the top.  Stir each well with a fork to coat the smoked salmon, onions, and capers with the eggs.
  4. Bake for 25 minutes, or until the egg muffins rise and set.  Allow the eggs to cool in the pan for 5 minutes, then run a knife around the edge of the wells and remove with a spoon.

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Smoked Salmon Egg Muffins: full of smoked salmon, capers, and red onion, these smoked salmon egg muffins are an easy, healthy low carb, high protein breakfast option. Make ahead and enjoy later!