Hearty Keto Ham and Cheese Bake

Here is my favorite keto ham and cheese breakfast bake recipe, with fluffy eggs, plenty of melted cheddar, diced ham, colorful peppers and onions, and a creamy mixture of heavy cream and sour cream.

This breakfast bake is my go-to for lazy weekend mornings when I want something hearty that feeds the whole family. I love that I can prep it the night before and just pop it in the oven while I’m making coffee. Plus, the leftovers reheat great all week long!

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What Kind of Ham Should I Use?

Any cooked ham you have on hand will work great for this breakfast bake. Leftover ham from a holiday dinner is perfect, but deli ham from the grocery store works just as well – just dice it up into bite-sized pieces. If you’re using deli ham, go for a thicker cut so you get nice chunky pieces throughout the bake rather than thin shreds. You can also use ham steak, which is usually found near the bacon at the store and is already the perfect thickness for dicing. Just avoid honey-glazed or heavily sweetened hams if you’re keeping things keto, and stick with plain or lightly smoked varieties.

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Options for Substitutions

This breakfast bake is easy to customize based on what you have in your kitchen:

• Ham: Cooked bacon, breakfast sausage, or turkey work great here. Just make sure whatever meat you use is fully cooked before adding it to the bake.
• Cheddar cheese: Feel free to mix it up with Monterey Jack, Colby, Swiss, or Gruyere. You can also do a blend of different cheeses if that’s what you have on hand.
• Heavy whipping cream: Half-and-half works in a pinch, though your bake will be slightly less rich. For a dairy-free option, try unsweetened coconut cream or almond milk, but note this will change the texture a bit.
• Sour cream: Greek yogurt (full-fat for keto) or cream cheese can step in here. If using cream cheese, soften it first and whisk it well with the eggs.
• Bell peppers and onions: Swap these with mushrooms, spinach, tomatoes, or jalapeños based on your preferences. Just keep the total amount of veggies similar to avoid adding too much moisture.
• Dry mustard: Regular prepared mustard works too – use about 1 teaspoon. Dijon mustard adds a nice tang if you have it.

Watch Out for These Mistakes While Baking

The biggest mistake with breakfast bakes is skipping the step of sautéing your peppers and onions first, which releases excess moisture that can make your casserole watery instead of firm and sliceable.

Another common error is adding all the cheese at once – save about half a cup to sprinkle on top during the last 10 minutes of baking for that golden, bubbly finish everyone loves.

Make sure your oven temperature isn’t too high, as eggs can become rubbery and tough when baked above 350°F, and always check the center with a knife around the 35-minute mark since ovens vary.

Let the casserole rest for at least 10 minutes after removing it from the oven, which allows it to set properly and makes cutting clean squares much easier.

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What to Serve With Ham and Cheese Breakfast Bake?

This breakfast bake is pretty filling on its own, but I love serving it with a simple side salad of mixed greens and cherry tomatoes to balance out the richness. A dollop of sour cream or some sliced avocado on top adds a nice cool, creamy contrast to the warm, cheesy eggs. If you’re feeding a crowd for brunch, consider adding some fresh berries or melon on the side for a touch of sweetness. You could also serve it with hot sauce or salsa for anyone who likes a little kick with their breakfast.

Storage Instructions

Store: This breakfast bake is a meal prep dream! Once it’s cooled down, cover the dish tightly with plastic wrap or foil and keep it in the fridge for up to 4 days. You can also slice it into individual portions and store them in separate containers for easy grab-and-go breakfasts throughout the week.

Freeze: Cut the bake into individual servings and wrap each piece in plastic wrap, then place them all in a freezer-safe container or bag. They’ll keep in the freezer for up to 2 months, which is great when you want a quick breakfast ready to go.

Reheat: For refrigerated portions, just microwave on medium power for about 1-2 minutes until warmed through. If you’re reheating from frozen, let it thaw in the fridge overnight first, or microwave on low power for 3-4 minutes. You can also reheat slices in the oven at 350°F for about 10-15 minutes if you want to crisp up the edges a bit.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 2300-2500
• Protein: 145-160 g
• Fat: 180-200 g
• Carbohydrates: 20-25 g

Ingredients

For the bake:

• 2 tbsp red peppers (finely diced)
• 1/2 cup heavy whipping cream
• 1/4 cup sour cream
• 2.5 cups shredded cheddar cheese (I prefer Cabot for better melting)
• 1/2 tsp smoked paprika
• 1 tbsp butter (melted)
• 1/2 tsp black pepper
• 1/2 tsp salt
• 2 tbsp green peppers (finely diced)
• 2 tbsp onion (finely diced)
• 14 eggs (large, room temperature)
• 1 tsp dry mustard
• avocado oil spray
• 2 cups diced cooked ham

For serving (optional):

• sour cream (optional, adds creamy richness)

Step 1: Prepare Mise en Place and Preheat Oven

• 2 tbsp red peppers
• 2 tbsp green peppers
• 2 tbsp onion
• 14 eggs

Preheat your oven to 350°F.

While it heats, finely dice the red peppers, green peppers, and onion, then set them aside on a cutting board.

Crack all 14 eggs into a large mixing bowl and let them sit at room temperature—this helps them incorporate more smoothly into the custard base.

Measure out the heavy whipping cream, sour cream, shredded cheddar cheese, and all dry seasonings (smoked paprika, black pepper, salt, and dry mustard) so everything is ready to go.

Having all your ingredients prepped and measured before you start cooking is the key to a smooth, stress-free breakfast bake.

Step 2: Sauté Vegetables and Prepare Baking Dish

• avocado oil spray
• 1 tbsp butter
• 2 tbsp red peppers
• 2 tbsp green peppers
• 2 tbsp onion

Spray a 9×13-inch baking dish with avocado oil spray, making sure to coat the bottom and sides evenly to prevent sticking.

Melt the butter in a skillet over medium heat, then add the diced peppers and onion.

Sauté for 4-5 minutes, stirring occasionally, until the vegetables are softened and slightly fragrant.

The goal here is to take the raw edge off the vegetables while they still maintain some texture—they’ll continue to cook in the oven, so don’t overdo it.

Step 3: Build the Egg Custard Base

• 14 eggs
• 1/2 cup heavy whipping cream
• 1/4 cup sour cream
• 1 tsp dry mustard
• 1/2 tsp salt
• 1/2 tsp smoked paprika
• 1/2 tsp black pepper

Add the heavy whipping cream, sour cream, dry mustard, salt, smoked paprika, and black pepper to the bowl with the room temperature eggs.

Whisk everything together vigorously for about 1-2 minutes until the mixture is well combined and slightly frothy—this incorporates air and creates a lighter, fluffier texture in the final bake.

I find that whisking by hand rather than using a blender gives you better control and a more delicate result.

Don’t worry about the eggs looking completely uniform; a few streaks are fine.

Step 4: Combine All Components

• sautéed vegetables from Step 2
• 2 cups diced cooked ham
• 2 cups shredded cheddar cheese
• egg custard mixture from Step 3

Add the sautéed vegetables from Step 2, the diced cooked ham, and 2 cups of the shredded cheddar cheese to the egg custard mixture from Step 3.

Fold everything together gently with a spatula or wooden spoon, being careful not to deflate the eggs too much.

The folding motion helps distribute the ingredients evenly without overdoing the mixing.

Once combined, pour the entire mixture into the prepared baking dish from Step 2, spreading it out into an even layer.

Step 5: Top and Bake

• 1/2 cup shredded cheddar cheese

Sprinkle the remaining 1/2 cup of shredded cheddar cheese evenly over the top of the egg mixture.

This creates a golden, crusty top layer that adds texture and extra cheesy flavor to each bite.

Place the baking dish in the preheated 350°F oven and bake for 50-60 minutes.

The bake is done when the center is set but still slightly jiggly (like a gentle wobble when you shake the dish), and the edges are golden brown.

A knife inserted in the center should come out mostly clean with just a tiny bit of creamy custard clinging to it—this means the residual heat will continue to cook it gently as it cools.

Step 6: Cool and Serve

• sour cream

Remove the baking dish from the oven and let it rest on the counter for 5-10 minutes before serving.

This resting period allows the custard to set up fully and makes it easier to cut into neat portions.

Serve warm or at room temperature.

If desired, top individual portions with a dollop of sour cream for added creaminess and brightness.

Hearty Keto Ham and Cheese Bake

Delicious Hearty Keto Ham and Cheese Bake recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 25 minutes mins

Cook Time 45 minutes mins

Total Time 1 hour hr 12 minutes mins

Servings 8 servings

Calories 2400 kcal

Ingredients

  

For the bake:

• 2 tbsp red peppers (finely diced)
• 1/2 cup heavy whipping cream
• 1/4 cup sour cream
• 2.5 cups shredded cheddar cheese (I prefer Cabot for better melting)
• 1/2 tsp smoked paprika
• 1 tbsp butter (melted)
• 1/2 tsp black pepper
• 1/2 tsp salt
• 2 tbsp green peppers (finely diced)
• 2 tbsp onion (finely diced)
• 14 eggs (large, room temperature)
• 1 tsp dry mustard
• avocado oil spray
• 2 cups diced cooked ham

For serving (optional):

• sour cream (optional, adds creamy richness)

Instructions

 

• Preheat your oven to 350°F. While it heats, finely dice the red peppers, green peppers, and onion, then set them aside on a cutting board. Crack all 14 eggs into a large mixing bowl and let them sit at room temperature—this helps them incorporate more smoothly into the custard base. Measure out the heavy whipping cream, sour cream, shredded cheddar cheese, and all dry seasonings (smoked paprika, black pepper, salt, and dry mustard) so everything is ready to go. Having all your ingredients prepped and measured before you start cooking is the key to a smooth, stress-free breakfast bake.
• Spray a 9x13-inch baking dish with avocado oil spray, making sure to coat the bottom and sides evenly to prevent sticking. Melt the butter in a skillet over medium heat, then add the diced peppers and onion. Sauté for 4-5 minutes, stirring occasionally, until the vegetables are softened and slightly fragrant. The goal here is to take the raw edge off the vegetables while they still maintain some texture—they'll continue to cook in the oven, so don't overdo it.
• Add the heavy whipping cream, sour cream, dry mustard, salt, smoked paprika, and black pepper to the bowl with the room temperature eggs. Whisk everything together vigorously for about 1-2 minutes until the mixture is well combined and slightly frothy—this incorporates air and creates a lighter, fluffier texture in the final bake. I find that whisking by hand rather than using a blender gives you better control and a more delicate result. Don't worry about the eggs looking completely uniform; a few streaks are fine.
• Add the sautéed vegetables from Step 2, the diced cooked ham, and 2 cups of the shredded cheddar cheese to the egg custard mixture from Step 3. Fold everything together gently with a spatula or wooden spoon, being careful not to deflate the eggs too much. The folding motion helps distribute the ingredients evenly without overdoing the mixing. Once combined, pour the entire mixture into the prepared baking dish from Step 2, spreading it out into an even layer.
• Sprinkle the remaining 1/2 cup of shredded cheddar cheese evenly over the top of the egg mixture. This creates a golden, crusty top layer that adds texture and extra cheesy flavor to each bite. Place the baking dish in the preheated 350°F oven and bake for 50-60 minutes. The bake is done when the center is set but still slightly jiggly (like a gentle wobble when you shake the dish), and the edges are golden brown. A knife inserted in the center should come out mostly clean with just a tiny bit of creamy custard clinging to it—this means the residual heat will continue to cook it gently as it cools.
• Remove the baking dish from the oven and let it rest on the counter for 5-10 minutes before serving. This resting period allows the custard to set up fully and makes it easier to cut into neat portions. Serve warm or at room temperature. If desired, top individual portions with a dollop of sour cream for added creaminess and brightness.