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    Home » Recipes » Breakfast

    Clean Keto Breakfast Casserole

    Published: Feb 21, 2024 · Modified: Feb 24, 2025 by Natalie Perry · This post may contain affiliate links · 2 Comments

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    Kick off your day with our Clean Keto Breakfast Casserole. It's the perfect recipe to meal-prep for those busy mornings when you want a nutritious, easy breakfast recipe without the hassle. It's the ideal mix of turkey sausage, uncured bacon, baby spinach, onions, and red bell peppers, all tied together with flavorful pepper jack cheese. Add a dollop of salsa or a splash of hot sauce for a satisfying finish.

    A white ceramic baking dish with a keto breakfast casserole, showing the baked casserole with a square piece being lifted out with a spatula, revealing the layers of egg, cheese, meat, and vegetables. this …

    I love creating easy low carb recipes like Keto Chicken and Rice Casserole, Keto Green Chile Chicken Casserole, and Cheesy Keto Italian Stuffed Peppers.

    This easy keto breakfast recipe is another gem in our keto collection. It's got the right mix of fluffy eggs, meats, and veggies to satisfy the whole family. This breakfast casserole is a delicious start to any day on a keto diet (or anyone looking to eat healthy whole-food meals.)

    The trick was to get the right ratio of ingredients without bread for the perfect high protein low carb casserole.

    For a variety of flavors check out our keto egg bites, or Starbucks egg white bites.

    Setting healthy intentions is the first step in your keto journey. For more guidance, our free guide to setting intentions and using affirmations is a great place to start.

    Check out our clean keto guide and meal plan for more low-carb inspiration.

    Jump to:
    • Ingredients for Clean Keto Breakfast Casserole
    • Substitutions and Variations
    • How to Make Clean Keto Breakfast Casserole
    • Storage
    • Top tip
    • Recipe FAQ's
    • More Keto Recipes
    • Recipe
    • Comments

    Ingredients for Clean Keto Breakfast Casserole

    An array of ingredients for a keto breakfast casserole neatly placed in white bowls on a wooden surface. Ingredients include cut turkey sausage links, shredded pepper jack cheese, crumbled bacon, whisked eggs, chopped red bell pepper, coconut cream, chopped spinach, and diced yellow onions.

    Eggs:  Organic eggs are a powerhouse of nutrition. For the freshest taste and highest quality, select eggs that are both "pasture-raised" and "organic."

    Pepper Jack Cheese: With its creamy texture and spicy flavor, this cheese is a delicious addition to our breakfast casserole. Buy a block and grate it yourself to avoid hidden carbs from added starches.

    Breakfast Sausage: I recommend uncured turkey or chicken sausage.

    Coconut Cream: Coconut cream is a great heavy cream alternative. It is rich and adds a velvety texture to the casserole. Find it next to the canned coconut milk in the grocery store, and stick with organic. It's even cheaper than the heavy cream (which often comes with a long list of ingredients).

    Red Peppers: Brighten up your casserole with red peppers, which bring a dose of vitamin A. Organic is best.

     Fresh Spinach: Packed with nutrients, fresh spinach is the perfect way to sneak in some leafy greens. Always opt for organic to avoid pesticides, especially since spinach is often on the dirty dozen list.

    Uncured Bacon: This ingredient adds a rich flavor without unwanted additives. Learn how to pick the best bacon for a keto diet, and always choose unsweetened, uncured, and organic.

    Substitutions and Variations

    Vegetables: Tailor the casserole to your personal preferences by adding different veggies. Think green onions, mushrooms, or even kale for a nutrient boost.

    Cheese: Swap out pepper jack for sharp cheddar cheese or go dairy-free by omitting cheese altogether. 

    Meat: Replace turkey sausage links with ground sausage or Italian sausage for a different flavor profile.

    Egg Bites: For portable breakfasts, add cottage cheese and pour the mixture into a muffin tin to create fluffy egg muffins. This bakes faster at only 25-30 minutes in the oven. Ideal for on-the-go meals or quick snacks.

    How to Make Clean Keto Breakfast Casserole

    Preheat Oven and Prepare Casserole Dish: Begin by setting your oven to 350°F (175°C). Using a bit of oil or butter, lightly coat the inside of a 9x13-inch baking dish to prevent sticking.

    A skillet with turkey sausage links and bacon strips being cooked, showing the sausage browned and bacon crispy.

    Step 1: Cook bacon in a large skillet over medium heat until crispy. Then, transfer the bacon to paper towels to drain and crumble into small pieces.

    Cook turkey sausage links in the same skillet until they're browned. Then, cut them into ½-inch slices.

    A skillet with sautéed vegetables for a keto breakfast casserole, showing diced onions, red bell peppers, and wilted spinach cooked down and ready to be layered into the casserole.

    Step 2: In the same skillet used for the meat, add your chopped onion and bell pepper.

    Saute these over medium heat until they've softened, which should take about 5 minutes.

    Introduce the spinach towards the end, just long enough for it to wilt, then remove it from the heat.

    Chopped vegetables including red bell peppers, onions, and spinach layered on top of the meat in a white ceramic baking dish, prepped for a keto breakfast casserole.

    Step 3: In your casserole dish, evenly lay out the sliced sausage and crumbled bacon. Follow this with an even layer of sautéed vegetables on top.

    A close-up view of a clear glass bowl with a whisked mixture of eggs, cream, shredded cheese, seasoned with salt and pepper, ready for a keto breakfast casserole. A black whisk is resting inside the bowl to mix the ingredients.

    Step 4: In a large mixing bowl, vigorously whisk together the eggs, coconut cream, and your seasonings including salt, pepper, and if you like, a bit of garlic powder. I like to use a hand mixer for this. After that, gently fold in the shredded cheese.

    A breakfast casserole in a red ceramic dish before baking, with the egg mixture poured over chopped meats and diced vegetables, all uncooked and ready to go into the oven.

    Step 5: Gently pour the egg and cheese mixture over the layered meats and vegetables in your baking dish. Make sure it is covered well. give it a gentle stir to make sure everything is mixed in.

    Baked breakfast casserole in a red ceramic dish showing a golden-brown crust on top with visible chunks of red bell pepper and green spinach scattered throughout.

    Step 6: Put the casserole in the oven. Bake for 35-40 minutes, or until the mixture is firmly set in the center and the top turns a delicious golden brown.

    Use a toothpick to check if done. It should come out clean. If the casserole is "sloshy" give it 5 more minutes!

    Cool and Serve: Before serving, allow the casserole to cool slightly in the dish. This step helps the egg mixture set properly, making the casserole easier to cut into individual portions.

    Hint: When using coconut cream, the best way to get just the cream is to scoop out the thick cream from the top of the can, leaving the lighter coconut water behind. Don't toss it! That coconut water makes a great addition to shakes or smoothies, adding a refreshing twist and extra hydration.

    Storage

    Refrigerator: For a more eco-friendly alternative, cover the casserole dish with beeswax wrap instead of traditional plastic wrap or aluminum foil, maintaining freshness.

    Freezer: To keep the casserole for up to 3 months place individual portions in freezer-safe airtight containers. To that, move the needed portion to the refrigerator the night before you plan to enjoy it.

    Reheating: For reheating, the oven or a skillet over medium heat are your best options. When using the oven, simply place the casserole or individual portions in an oven-safe dish, covering it with a baking sheet or an oven-safe lid to retain moisture, and heat at 350°F until thoroughly warmed.

    Top tip

    When preparing the egg mixture for your clean keto breakfast casserole, consider using an immersion blender to combine the eggs and coconut cream. This technique ensures a smooth, thoroughly mixed base, enhancing the fluffy texture of your casserole. Just remember to blend before adding the cheese.

    Recipe FAQ's

    What is a typical keto breakfast?

    A typical keto breakfast focuses on low carb, high-fat foods to keep you in ketosis. It often includes eggs, avocados, and meats like bacon or sausage. Many also enjoy dairy products like cheese and full-fat yogurt. Keto-friendly vegetables like spinach or kale can add fiber and nutrients. Breakfasts can range from simple eggs and bacon to keto pancakes or muffins made with almond or coconut flour. Chia seed pudding with full-fat coconut milk works well too! As long as you use monk fruit or stevia for the sweetener and be mindful of your toppings!

    Can I have 3 eggs for breakfast on keto?

    Yes, you can have 3 eggs for breakfast on a keto diet. Eggs are an excellent source of protein and healthy fats, making them ideal for keto. They're also very versatile, allowing for various preparations like boiled, scrambled, or as part of an omelet with keto-friendly vegetables and meats. Just be mindful of what you pair them with to keep your overall carb intake low.

    What are the top 5 keto foods?

    The top 5 keto foods that are staples for anyone following the ketogenic diet include:
    Avocados: Rich in healthy fats and fiber, avocados are perfect for keto. They can be eaten alone, used in recipes, or as a topping.
    Eggs: Highly versatile and packed with protein, eggs are essential for keto breakfasts and meals.
    Meats: Fatty cuts of meat like steak, pork, chicken thighs, and especially grass-fed and organic options are keto favorites for their high protein and fat content.
    Leafy Greens: Spinach, kale, and other leafy greens are low in carbs but high in fiber and nutrients, making them ideal for adding volume and vitamins to your meals without adding carbs.
    Cheese: Full-fat cheeses are a delicious way to add fat and flavor to your keto diet. Shred your own cheese helps to avoid hidden starches.

    A full keto breakfast casserole in a red ceramic baking dish displayed on a wooden table, showing a top view of the baked, golden-brown crust with visible herbs.

    More Keto Recipes

    These are some of my favorite low-carb/ keto recipes:

    • Freshly baked stuffed bell peppers in a casserole dish, cheese melted and slightly browned, garnished with finely chopped basil.
      Cheesy Keto Italian Stuffed Peppers with Cauliflower Rice
    • Two egg white bites on a plate with visible chunks of green onion, red bell pepper, and spinach, with a silver fork on the side
      Starbucks Egg White Bites in the Oven
    • Plated serving of keto chicken and cauliflower rice casserole garnished with avocado and tomato
      Bacon Ranch Keto Chicken and Rice Casserole
    • A portion of Keto Spinach Artichoke Chicken Casserole on a plate with asparagus, showcasing the creamy filling.
      Keto Spinach Artichoke Chicken Casserole

    Did you try our clean keto breakfast casserole? Let us know how you liked it in the comments below! Don't forget to leave a 🌟 rating! Subscribe to our weekly newsletter for all the best healthy recipes in your inbox. I look forward to hearing from you!

    Recipe

    A full keto breakfast casserole in a red ceramic baking dish displayed on a wooden table, showing a top view of the baked, golden-brown crust with visible herbs.

    Clean Keto Breakfast Casserole

    Natalie Perry
    This Clean Keto Breakfast Casserole is the perfect low-carb start to your day. An easy recipe that's ideal for those on a low-carb diet, it is a satisfying make-ahead breakfast perfect for busy mornings. Packed with protein and healthy fats, it's a savory keto breakfast to keep you energized.
    5 from 36 votes
    Print Recipe Pin Recipe
    Prep Time 15 minutes mins
    Cook Time 40 minutes mins
    Total Time 55 minutes mins
    Course Breakfast
    Cuisine American
    Servings 8
    Calories 434 kcal

    Equipment

    • 9x13 inch baking dish
    • large skillet
    • Large Mixing Bowl
    • Immersion blender, high-speed blender, or food processor
    • Cheese grater (if grating cheese yourself)

    Ingredients
      

    • 6 oz turkey or chicken breakfast sausage cut into ½ inch pieces
    • 8 slices uncured bacon crumbled
    • 12 eggs pasture-raise, organic
    • 1 cup coconut cream organic, canned
    • 2 cups pepper jack cheese organic, shredded (from a block to avoid preservatives)
    • 1 yellow onion medium, finely chopped
    • 1 red bell pepper organic, diced
    • 1 cup fresh spinach organic
    • 1 teaspoon sea salt
    • ½ teaspoon black pepper organic
    • Optional: ½ teaspoon garlic powder
    Get Recipe Ingredients

    Instructions
     

    • Preheat Oven and Prepare Pan: Heat your oven to 350°F (175°C). Grease a 9x13 inch baking dish lightly.
    • Cook Meats: In a large skillet over medium heat, cook the bacon until crispy. Transfer to paper towels to drain, then crumble. In the same skillet, cook the sausage pieces until browned. Transfer to the prepared baking dish.
    • Sauté Vegetables: In the skillet, add the onion and bell pepper, cooking until soft, about 5 minutes. Add spinach until just wilted. Evenly spread the vegetable mixture over the meat in the baking dish.
    • Mix Eggs and Cream: In a large mixing bowl, blend the eggs and coconut cream using an immersion blender, high-speed blender, or food processor until smooth. Stir in the shredded cheese by hand.
    • Assemble Casserole: Pour the egg and cheese mixture over the sausage, bacon, and vegetables in the dish. Ensure even coverage.
    • Bake: Bake in the preheated oven for 35-40 minutes, until the casserole is set and the top is lightly golden.
    • Cool and Serve: Let the casserole cool slightly before serving. Garnish with hot sauce, sour cream, and avocados to enhance the flavors.

    Video

    Notes

    • Using an immersion blender for the eggs and cream can help achieve a smoother, more cohesive mixture.
    • When using coconut cream, open the can and carefully scoop out the cream on top to get the creamiest parts of it and not the watery part.
    • This casserole is perfect for meal prep. Store leftovers in the fridge and reheat on the stovetop, covered, for a delicious meal on a busy day.

    Nutrition

    Calories: 434kcalCarbohydrates: 5gProtein: 24gFat: 36gSaturated Fat: 20gPolyunsaturated Fat: 4gMonounsaturated Fat: 10gTrans Fat: 0.1gCholesterol: 301mgSodium: 831mgPotassium: 385mgFiber: 1gSugar: 2gVitamin A: 1416IUVitamin C: 22mgCalcium: 265mgIron: 3mg
    Tried this recipe?Let us know how it was!

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    Comments

      5 from 36 votes (35 ratings without comment)

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      Recipe Rating




    1. Alexandra says

      February 22, 2024 at 9:16 pm

      5 stars
      This was perfect for my meal prep - simple to prepare, tasty and protein packed. It made for a delicious start to the day.

      Reply
      • Natalie Perry says

        February 23, 2024 at 5:08 pm

        Happy you are enjoying the breakfast casserole, too!

        Reply
    A woman smiling with long brown hair and flowered v-neck dress shirt on.

    Hello there! My name is Natalie. My passion is creating and sharing healthy recipes, tips, and affirmations for a healthy mind and body. I am a wife, mom, certified holistic nutrition specialist, hypnotherapist, reiki master, and healthy food blogger! I enjoy learning, creating, and sharing healthy recipes that the whole family will love.

    Thanks for stopping in! We look forward to hearing how you like our recipes! Welcome to the tribe :)

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    A Pinterest-style image showcasing a completed Keto Meal Prep Breakfast Casserole with text overlays. The top photo shows the casserole in a red baking dish with a golden-brown top, and the bottom photo displays a plated piece of the casserole revealing the colorful layers of vegetables and meat. The text reads "Keto Meal Prep Breakfast Casserole" with the website "mindfullyhealthyliving.com" at the bottom.

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