On the Go! Crustless Chipotle Egg Cups

I love these Crustless Chipotle Egg Cups (or as some people call them breakfast egg muffin cups). They are my “go to” for an easy meal prep breakfast. You can make a batch in under an hour, freeze them for later and have a quick breakfast for 24 days! I eat one for breakfast with a banana and a hot cup of tea. I even take them in a cooler frozen when traveling.

Previously published on March 13, 2018, updated with new pictures and information.

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Quick easy breakfast in 1 1/2 min! Low in WW Points

Of course these healthy breakfast egg cups with ham are best in my opinion right out of the oven but they still are delicious reheated for a quick breakfast.  Just pop them into the microwave for about 1 1/2 minutes. Serve one with a bowl of fresh fruit and you have a delicious and filling breakfast. Only 1 Smart Point per cup with the Freestyle Weight Watcher Plan! If you want to shave off more calories, just leave out the cheese, ham or bacon. I tend to like a lot of protein in mine and since I only eat one for breakfast, 101 calories per cup is fine for me.

Add in your own ingredients!

Make it your own by adding other ingredients such as spinach, red pepper, broccoli, chives – whatever you desire! You can switch up the cheese as well. Try to stick to the same amount though if you’re looking to keep the calories down. My favorite ones are by far- the egg cups with ham. I’ll add other things but I have to have the ham!

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FAQ About Healthy Breakfast Egg Muffin Cups:

Can you meal prep eggs?

Yes, these definitely make a great meal prep egg breakfast! Make a batch and have breakfast for 24 days or make a double batch and you’ll be set for a long time!

Will eggs stick to cupcake liners?

I find that if you use cupcake lines, they stick. The best way to make these egg cups is to use Silicone Muffin Cups and spray them heavily with a non-stick cooking spray. I usually like to use my oil mister but in this case, it’s better to use non-stick cooking spray as they will stick.

How do you use freeze egg cups?

Allow them to cool (take them out of silicone muffin cups) on a baking sheet lined with parchment paper. Then “flash freeze,” in freezer until frozen. Remove and transfer to vacuum sealed bags or plastic bags.

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How to Make Chipotle Egg Cups in Pictures:

Food processor bowl with ham, garlic, jalapenos on a granite counter from Gourmet Done Skinny

Combine garlic, onion, ham and jalapeño in a food processor. Pulse until finely chopped.

Nutrimill Artiste Mixer with eggs, ham, bacon, jalapeno and spices from Gourmet Done Skinny

In a mixing bowl, (mine is the Nutrimill Artiste Mixer – love that one!), combine eggs, bacon, ham mixture, salt, pepper and homemade chipotle seasoning.

2 red silicone muffin cups on a granite counter with cooking spray from Gourmet Done Skinny

Spray silicone muffin cups with cooking spray. In this case I don’t recommend the olive oil mister. The non-stick cooking spray does the best job to prevent the egg cups from sticking.

Red silicone muffin cup filled with egg mixture and cheese sprinkled on top from Gourmet Done Skinny

Scoop about 1/4 c. of egg mixture into each cup. Try a get a little of the “good stuff,” at the bottom of the bowl for each egg cup. Distribute the shredded cheese evenly over each cup.

Red silicone muffin with baked Chipotle Egg Cups from Gourmet Done Skinny

Bake in a preheat 350° oven for 18-30 minutes. All ovens are different, mine takes about 18 minutes because it’s convection but my parent’s oven takes about 25. Just watch and bake until set.

Red silicone muffin cups on a baking sheet lined with parchment paper

Allow egg cups to cool for about 5 minutes. Set a timer. Then remove by sliding a knife around the egg and using a fork to lift out the cup.

Chipotle Egg Cups on a pan zoomed in

Allow to cool, then flash freeze on a baking sheet lined with parchment paper until solid.

Chipotle Egg Cups packaged in bags

Store in vacuum sealed bags in the freezer.

Delicious Chipotle Egg Cups ready to eat on a wooden board with red onion, egg, garlic, bacon and jalapeno in the background from Gourmet Done Skinny

When ready to eat, microwave for about 1 minute and serve with a side of fruit. Enjoy your breakfast on the go!

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Delicious Chipotle Egg Cups ready to eat on a wooden board with red onion, egg, garlic, bacon and jalapeno in the background from Gourmet Done Skinny

On the Go! Crustless Chipotle Egg Cups

  • myWW Points:Blue 1 Smart Point; Green program 3 Smart Points; Purple 1 Smart Point
  • Author: Gourmet Done Skinny
  • Prep Time: 15
  • Cook Time: 18-25 depending on oven
  • Total Time: about 40 minutes
  • Yield: 24 egg cups 1x
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American


Make up a batch of these Crustless Chipotle Egg Cups and always have breakfast ready in a jiffy!  I routinely make a batch or two of these and flash freeze them on a cookie sheet, then transfer to ziplock bags in my freezer. When I need breakfast, I microwave one for 1 min 15 seconds.  Packed with protein and goodness for only 1 point! One thing to note, use silicone muffin pans.  They “pop” right out! Otherwise you spend too much time cleaning the metal tins even if you spray them heavily.



  • 20 whole eggs
  • 3 cloves garlic
  • 1/4 c. onion
  • 6 oz ham
  • 1/2 jalapeño
  • 1/2 t. kosher salt
  • black pepper to taste
  • 12 T. crumbled bacon (I like to use the Kirkland brand from Costco)
  • 1 T. Chipotle Seasoning, or use whatever you like
  • 4 oz reduced cheddar, shredded (about 1 cup shredded)
  • non-stick cooking spray (on this one use Pam or I use the Kirkland brand – not the olive oil spray from mister-see notes)


  1. Preheat oven to 350°. Spray silicone muffin cups (2 sets of 12) with cooking spray and place cups on a cookie sheet.
  2. In a food processor (or chop by hand), combine: garlic, onion, ham and jalapeño. Lightly pulse until finely chopped.
  3. In a large mixing bowl, mix eggs, salt and pepper, chipotle seasoning and bacon. I like to use my Nutrimill Artiste Mixer.
  4. Scoop about 1/4 c. of egg mixture into each cup. Try a get a little of the “good stuff,” at the bottom of the bowl for each egg cup. Distribute the shredded cheese evenly over each cup.
  5. Bake 18-30 min until set. You don’t want them overdone. Every oven is different. If you use a convection oven, bake time is about 18 min, where as a regular oven may take up to 30 min. Take them out when they don’t, “jiggle,” when you gently shake the pan.
  6. Allow egg cups to sit 5 minutes before removing them to platter.
  7. Carefully remove each egg cup with two forks on either side, or sometimes I run a knife around each up before I pull them out. Transfer to a plate to cool.
  8. When cool, transfer to a cookie sheet and place in the freezer. Flash freeze for at least 10-20 min then put into vacuum sealed bags.
  9. When ready to eat, place egg cup on a plate and microwave for about 1 minute 15 seconds. Or if you have time reheat in toaster oven until warm.


This recipe was adapted from Skinnytaste Loaded Baked Omelet Muffins. I just love Gina’s recipes! Check her out! Usually I like to use olive oil from my Olive Oil Sprayer but in this case, non-stick cooking spray works much better. The egg mixture sticks when you use the olive oil sprayer.

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