Low Carb Chicken Fajita Casserole Meal Prep – Flavor-Packed, Weeknight-Friendly

This casserole gives you all the smoky, zesty goodness of chicken fajitas without the tortillas or fuss. It’s simple to make, holds up beautifully for meal prep, and delivers bold flavor in every bite. You’ll layer juicy chicken, sweet peppers, and onions under a creamy, cheesy topping that bakes bubbly and golden.

It’s comforting, low carb, and easy to customize for your spice level and pantry. Make it once, and lunch for the week is done.

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Low Carb Chicken Fajita Casserole Meal Prep - Flavor-Packed, Weeknight-Friendly

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Prep Time 15 minutes mins

Cook Time 30 minutes mins

Total Time 45 minutes mins

Servings: 4 servings

Ingredients Method

Ingredients

  

• 1.5 pounds boneless, skinless chicken breasts, thinly sliced
• 3 bell peppers (mix of red, yellow, and green), thinly sliced
• 1 large yellow onion, thinly sliced
• 2 tablespoons olive oil, divided
• 1 tablespoon fresh lime juice (plus extra wedges for serving)
• 1 teaspoon lime zest (optional, but brightens flavor)
• 2 teaspoons chili powder
• 1 teaspoon ground cumin
• 1 teaspoon smoked paprika (or regular paprika)
• 1/2 teaspoon garlic powder
• 1/2 teaspoon onion powder
• 1/4 teaspoon dried oregano
• 1/4 to 1/2 teaspoon cayenne pepper (to taste)
• 1 teaspoon kosher salt, plus more to taste
• 1/2 teaspoon black pepper
• 4 ounces cream cheese, softened
• 1/2 cup plain Greek yogurt (or sour cream)
• 1/2 cup shredded Mexican blend or cheddar cheese
• 1/4 cup chopped fresh cilantro (optional)
• 1 jalapeño, thinly sliced (optional for heat)
• Avocado slices, for serving (optional)

Method

 

1. Preheat and prep: Heat the oven to 400°F (200°C). Lightly grease a 9x13-inch casserole dish. Pat chicken dry with paper towels.
2. Mix the fajita seasoning: In a small bowl, combine chili powder, cumin, smoked paprika, garlic powder, onion powder, oregano, cayenne, salt, and black pepper.
3. Season the chicken: Toss sliced chicken with half of the seasoning mix, 1 tablespoon olive oil, and lime zest. Set aside.
4. Sauté the veggies: Heat the remaining 1 tablespoon olive oil in a large skillet over medium-high. Add peppers and onions with a pinch of salt. Cook 5–7 minutes, tossing occasionally, until softened with a little char. Transfer to the casserole dish.
5. Quick sear the chicken: In the same hot skillet, add the seasoned chicken in a single layer. Sear 2–3 minutes per side until just opaque on the outside (it will finish in the oven). Scatter the chicken over the peppers and onions.
6. Make the creamy topping: In a bowl, whisk cream cheese and Greek yogurt until smooth. Stir in the remaining fajita seasoning and lime juice. Spread this mixture evenly over the chicken and veggies.
7. Add cheese and bake: Sprinkle shredded cheese over the top. Bake 15–18 minutes, until bubbly and the chicken reaches an internal temperature of 165°F (74°C).
8. Finish and rest: Let the casserole rest 5–10 minutes. Top with chopped cilantro and sliced jalapeño if using. Taste and adjust salt or a squeeze of lime.
9. Portion for meal prep: Divide into 4–5 airtight containers. Add avocado on the side, not on top, to keep it fresh.

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Why This Recipe Works

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• Low carb without sacrifice: You get the fajita flavor you crave—chile, lime, and smoky seasoning—without the starch.
• Meal-prep friendly: The texture improves as it sits, and it reheats well without drying out.
• One pan, minimal mess: A quick skillet sear for the veggies, then everything bakes together in one casserole dish.
• Balanced and filling: Protein-rich chicken plus fiber from peppers and onions keeps you satisfied longer.
• Flexible toppings: Add cheese, avocado, jalapeños, or a dollop of Greek yogurt to match your macros and taste.

Ingredients

• 1.5 pounds boneless, skinless chicken breasts, thinly sliced
• 3 bell peppers (mix of red, yellow, and green), thinly sliced
• 1 large yellow onion, thinly sliced
• 2 tablespoons olive oil, divided
• 1 tablespoon fresh lime juice (plus extra wedges for serving)
• 1 teaspoon lime zest (optional, but brightens flavor)
• 2 teaspoons chili powder
• 1 teaspoon ground cumin
• 1 teaspoon smoked paprika (or regular paprika)
• 1/2 teaspoon garlic powder
• 1/2 teaspoon onion powder
• 1/4 teaspoon dried oregano
• 1/4 to 1/2 teaspoon cayenne pepper (to taste)
• 1 teaspoon kosher salt, plus more to taste
• 1/2 teaspoon black pepper
• 4 ounces cream cheese, softened
• 1/2 cup plain Greek yogurt (or sour cream)
• 1/2 cup shredded Mexican blend or cheddar cheese
• 1/4 cup chopped fresh cilantro (optional)
• 1 jalapeño, thinly sliced (optional for heat)
• Avocado slices, for serving (optional)

Instructions

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1. Preheat and prep: Heat the oven to 400°F (200°C). Lightly grease a 9×13-inch casserole dish.

   Pat chicken dry with paper towels.

2. Mix the fajita seasoning: In a small bowl, combine chili powder, cumin, smoked paprika, garlic powder, onion powder, oregano, cayenne, salt, and black pepper.
3. Season the chicken: Toss sliced chicken with half of the seasoning mix, 1 tablespoon olive oil, and lime zest. Set aside.
4. Sauté the veggies: Heat the remaining 1 tablespoon olive oil in a large skillet over medium-high. Add peppers and onions with a pinch of salt.

   Cook 5–7 minutes, tossing occasionally, until softened with a little char. Transfer to the casserole dish.

5. Quick sear the chicken: In the same hot skillet, add the seasoned chicken in a single layer. Sear 2–3 minutes per side until just opaque on the outside (it will finish in the oven).

   Scatter the chicken over the peppers and onions.

6. Make the creamy topping: In a bowl, whisk cream cheese and Greek yogurt until smooth. Stir in the remaining fajita seasoning and lime juice. Spread this mixture evenly over the chicken and veggies.
7. Add cheese and bake: Sprinkle shredded cheese over the top.

   Bake 15–18 minutes, until bubbly and the chicken reaches an internal temperature of 165°F (74°C).

8. Finish and rest: Let the casserole rest 5–10 minutes. Top with chopped cilantro and sliced jalapeño if using. Taste and adjust salt or a squeeze of lime.
9. Portion for meal prep: Divide into 4–5 airtight containers.

   Add avocado on the side, not on top, to keep it fresh.

Keeping It Fresh

• Cool before sealing: Let portions cool to room temp for 15–20 minutes before lidding to prevent condensation and sogginess.
• Storage: Refrigerate in airtight containers for up to 4 days. For longer storage, freeze individual portions for up to 2 months.
• Reheating: Microwave 1.5–3 minutes, stirring halfway, until hot. Or reheat in a 350°F (175°C) oven for 10–12 minutes, covered.
• Fresh toppers: Add avocado, extra lime, or chopped cilantro after reheating for a just-cooked taste.

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Health Benefits

• High protein: Chicken breast provides lean protein to support muscle maintenance and satiety.
• Low carb, high fiber veggies: Bell peppers and onions bring fiber, vitamin C, and antioxidants with minimal carbs.
• Smart fats: Olive oil and optional avocado offer heart-healthy monounsaturated fats that help with fullness.
• Probiotic boost: Greek yogurt adds protein and beneficial cultures while keeping the sauce light and tangy.
• Sodium control: Season from scratch so you can manage salt better than with store-bought mixes.

What Not to Do

• Don’t skip drying the chicken: Excess moisture prevents a good sear and can water down the casserole.
• Don’t overcook in the skillet: Just sear; the oven finishes the job.

  Overcooking leads to dry, stringy chicken.

• Don’t bury it in cheese: Too much cheese can mask flavors and add heavy calories. Stick to the measured amount.
• Don’t add avocado before storing: It browns and gets mushy. Add fresh after reheating.
• Don’t forget acid: A squeeze of lime at the end brightens everything and balances the creamy topping.

Variations You Can Try

• Spicy chipotle: Swap smoked paprika for chipotle powder and add chopped canned chipotle in adobo to the creamy topping.
• Extra veggies: Stir in sliced mushrooms or zucchini with the peppers.

  Sauté to reduce moisture before baking.

• Dairy-light: Use reduced-fat cream cheese and Greek yogurt. Skip or reduce the shredded cheese and top with more cilantro and lime.
• Tex-Mex ranch: Mix 1 tablespoon ranch seasoning into the creamy topping and add a sprinkle of green onions after baking.
• Chicken thighs: Swap breasts for boneless, skinless thighs for extra tenderness. Trim visible fat to keep it leaner.
• Cauliflower rice base: For bigger portions without more carbs, spread a thin layer of sautéed cauliflower rice in the dish before adding the veggies and chicken.