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.