Southwest Breakfast Bake

This recipe is high protein, gluten free, and made with natural sugar
Servings: 10
Jump to Recipe
Time: 45 mins

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Southwest Egg Bake with piece taken out of skillet

This Southwest Egg Bake is spicy, creamy, and the perfect weekday breakfast meal prep or Sunday morning breakfast. It is ready in less than an hour, packed with protein, and filled with flavor!  It only takes one bowl and can be kept in the fridge for one week, perfect for meal prep!  It’s gluten free and made with only natural sugar!


Southwest Egg Bake Ingredients:

Quick Look at Making Southwest Egg Bake:

  1. Prep the veggies and preheat oven!  Dice, chop, and prep vegetables (including chipotles) and set oven to 350 degrees.
  2. Sauté onions and garlic!  In a pan with a little ghee or oil.  Make the house smell good! 
  3. Brown sausage in the pan with the onions and garlic. While this is cooking, whisk the eggs, milk, and seasonings in a bowl. 
  4. Add both peppers to pan with sausage mixture.  Yup, add both bell peppers and fresno chilis.  Cook until softened, usually 1-2 minutes. Add in chipotles after.
  5. Combine egg mixture, sausage mixture, and half the cheese into a 9×9 baking dish.  Mix them up!
  6. Bake for 25-30 minutes.  
  7. Top with remaining cheese after 25 minutes.  Turn to broil for 2-3 minutes to get that crispy top.  Let cool and enjoy!


Southwest Egg Bake Quick Facts

Does this meet my dietary needs? 

This recipe is gluten free and refined sugar free.

How many bowls should I plan for this meal? 

One bowl, one pan, and one baking dish.

How long does this keep? 

1 week in the fridge, 2 months in freezer.

How do I reheat this? 

Heat in microwave for 1-2 minutes or in toaster oven at 300 degrees for 5-10 minutes, until heated through.

Can I pack this for lunch?

Yup!  Just keep semi cold since this has meat and dairy in it.

Where do I find cumin and chipotles? 

Thankfully, all of these can both be found at Target, Walmart, Whole Foods, or similar.  They can also be found on amazon at the links below, yeah for convenience!  Cumin & chipotles.

Substitution Options

Spicy Sausage: Plain or breakfast chicken, turkey, or pork sausage can be used.  If using breakfast sausage, reduce salt added.  If using plain sausage, add additional chipotle peppers.

Fresno Chilis: Jalapenos, habaneros, or any other spicy peppers can be used.  If you cannot get fresh peppers, cayenne and chili powder can also be used.  These can also be left out to lower the spice level.

Milk:  Our favorite is Fairlife, but oat milk or flax milk can be used as a dairy free option.

Pepper Jack:  Shredded cheddar cheese can be used in place of pepper jack.  This recipe calls for a small amount of cheese, but up to 1 cup can be added if you are ok with cheese or just prefer more.  Dairy free cheese can also be used.

Butter:  We love Land O Lakes and Kerrygold butter, but ghee or coconut oil could be used too.  

Cumin:  Chili powder has cumin in it, along with a couple other ingredients.  Taste as you go when using this to not have too much of the other seasonings.  Coriander is also from the same plant and can be used as a sub as well.  Cumin can also be bought here.

Chipotle Peppers: Cayenne, red pepper flakes, or additional fresno chilis can be used in place.  Chipotle sauce, like this one, can also be used in place. If using chipotle peppers, we love these ones.

Fun Fact! 

Fresno Chilis were developed in 1952.  They were named after the town of Fresno, CA (the big city I grew up shopping in!).  They are considered to have a mid range spice level.  The heat in peppers comes from the chemical compound called capsaicin.  It has been known to reduce inflammation and promote a feeling of being full!  (Source)

Note: Joy to the Food gets commissions for purchases made through links in this post.


Try these other delicious recipes!

Flat Beef Enchiladas

Egg White Wrap

Chipotle Southwest Sauce

Homemade Chipotle Bowl

Southwest Egg Bake In a skillet

Southwest Egg Bake

Servings: 10
Total Time: 45 minutes
Start your morning off right with this Southwest Egg Bake! It's packed with protein and big, bold flavor.
5 from 4 votes
Print Pin Rate
Course: Breakfast
Cuisine: American, Mexican
Keyword: egg bake, gluten free, southwest, spicy, zero processed sugar
Prep Time: 15 minutes
Cook Time: 30 minutes
Total Time: 45 minutes
Calories: 276 kcal


  • 2 tbsp ghee or butter
  • 1 tbsp garlic minced
  • 1 white onion diced
  • 1 lbs hot sausage* *see notes below
  • 8 eggs
  • 1-1/2 tsp pepper
  • 1-1/2 tsp salt
  • 1/2 cup cheese
  • 1 cup milk
  • 1 bell pepper diced
  • 1 fresno chili diced
  • 1 tbsp paprika
  • 1 tbsp oregano
  • 1 tbsp cumin* *see notes below
  • 2 chipotle peppers in adobe sauce* *see notes below


  • Preheat oven to 350 degrees. Chop and wash vegetables to prep, including chipotle peppers if using whole chipotle.  Heat pan on medium high heat to melt ghee or butter.  Add diced onions and garlic and sauté until soft, usually 2-3 minutes.
  • Add sausage and cook until sausage is browned, approximately 10 minutes.  Meanwhile, whisk eggs, milk, and seasoning in a bowl, except chipotle peppers.
  • Add bell pepper and fresno chili to sausage mixture and cook for another 1-2 minutes, then mix in chipotle peppers
  • Pour sausage mixture into 9x9 baking pan
  • Add egg mixture and half of the cheese to baking pan, mix or stir to combine egg mixture and sausage mixture.
  • Bake for 25-30 min
  • At 25 minutes, remove bake from oven and sprinkle remaining cheese on top. Turn oven to High Broil and return bake to oven for 2-3 min to melt cheese and crisp the top. 
  • Let cool and enjoy!



Nutritional Information is an estimate and for informational purposes only.
*Note: substitution options can be found above in the substitution section of this post.
*What if I cannot find spicy sausage?
Plain sausage can be used with the addition of one Fresno chili (or chili of choice) and additional salt and pepper.  Seasoned sausage can also be used (Italian or other).  When using seasoned sausage, just add one additional chili of choice.  Chicken or turkey sausage can also be used with the same methods listed above.
*Can I use chipotle powder?
Yes!  Use 1 tablespoon chipotle powder in place whole chipotles
*What do I do if I can’t find cumin?
Cumin is a earthy distinct flavor found in most Mexican food.  It can be substituted with the same amount ground coriander.  Coriander and cumin come from the same plant family and have similar earth profiles.  If you cannot get coriander, you can substitute with the same amount of chili powder.  HOWEVER - chili powder is a combination of oregano, cayenne, garlic powder, and cumin, so you will need to cut the quantity of oregano, Fresno chili, and garlic by half.  2 tablespoons of taco seasoning can also be used in place of oregano, chipotle, cumin, salt, and pepper.  Check the ingredients on the taco seasoning also because it may have garlic and onion powder, in which case you would decrease the amount of garlic and onion by half.  If it is a spicy one, you would omit or decrease the amount of chili used.
Do I have to use Fresno chilis?  
No!  But, I do love the flavor.  Changing the type of pepper will change the heat level and flavor profile, just an fyi.
What should I bake it in if I only want a quarter or half batch?
We make half batches all the time and have great success with using a bread pan.  The other option for a quarter, third, or half batch is glass Tupperware (Pyrex or similar).  This is great because it already has a lid so it is ready as meal prep nearly right out of the oven.  Just double check that the specific glass is rated for oven baking temperatures and let the bake cool completely before placing in the fridge.  Placing a hot glass container in the refrigerator can cause the glass to crack or even burst due to the extreme change in temperature.  
Can I use other vegetables? 
Yes!  Use what you have on hand, some tomatoes would be great!  
Can this be vegetarian?
Yes!  If making vegetarian, omit the pork sausage.  You can sub mushrooms or leave as is.
Can this be dairy free? 
Yes!  To make dairy free, either omit the cheese or substitute for dairy free cheese, and swap the milk for an unflavored non-dairy milk, a lactose free milk, or water.  If using non-dairy milk, choose the type of milk carefully.  I have had the best luck with flax milk when substituting for savory dishes.  This has not been tested with non-dairy milk, only lactose free.  If you try it, leave a comment and let us know how it went!


Calories: 276kcal | Carbohydrates: 7g | Protein: 14g | Fat: 21g | Saturated Fat: 9g | Cholesterol: 180mg | Sodium: 738mg | Potassium: 261mg | Fiber: 2g | Sugar: 4g | Vitamin A: 748IU | Vitamin C: 19mg | Calcium: 111mg | Iron: 2mg
Did you try this? We'd love to hear how it went. Please leave a review below! Or, follow and tag us on Instagram!Mention @_Joytothefood_ or tag #joytothefood!


  1. Kelly White

    I made this recipe and it was great! I didn’t have Fresno peppers, so used jalapeño – just a bit. Also substituted regular Jimmy Dean sausage, and it was plenty spicy. Easy to make and delicious!

    • Dan Kinney

      Hi Kelly,

      We’re glad to hear the jalapeno and Jimmy Dean sausage substitute worked well for you. Thanks for sharing!

      -Dan & Mika

  2. Kelly

    5 stars
    Tried it with bacon instead of sausage, jalapeños (just a bit), and chili garlic sauce (didn’t have chipotle, or Fresno chilis) and paired it with the Immunity Smoothie. Awesome Saturday breakfast!

  3. KW

    5 stars
    Breakfast treat today! Awesome!

  4. Doug MacGibbon

    5 stars
    Great recipe. This is a great site for all recipe ideas!


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Welcome to Joy to the Food! We’re so glad you’re here. We’re Mika and Dan, and the two Nalas (our spunky pups). We’re all about easy and affordable recipes that bring joy to the kitchen and make life stress free!