Hearty Keto Ham and Cheese Bake

When I started eating keto, I thought I’d have to give up the comfort of a good breakfast casserole. Boy, was I wrong. This ham and cheese breakfast bake has become my go-to for weekend mornings and meal prep Sundays alike. It’s packed with eggs, cheese, and ham, so it keeps me full until lunch without any of the carb crash.

The best part? You can throw this together in one dish, bake it, and have breakfast sorted for the entire week. I love making it on Sunday night so Monday morning doesn’t feel quite so Monday. Just reheat a slice, maybe add a dollop of sour cream, and you’re good to go.

If you miss those classic breakfast flavors but want to stick to your keto goals, this one’s for you. It tastes like the breakfast bakes I grew up with, just without the bread or potatoes weighing you down.

What Kind of Ham Should I Use?

For this breakfast bake, you have a lot of flexibility when it comes to choosing your ham. Leftover baked ham from a holiday dinner works great and is a perfect way to use up extras, but deli ham from the grocery store is just as good and super convenient. If you’re using deli ham, grab about a pound of thick-cut slices and dice them up into bite-sized pieces. You can also use ham steak, which is usually found near the bacon in the meat section and is already the perfect thickness for cubing. Just avoid honey-baked or heavily glazed hams since the extra sweetness can throw off the savory flavor profile of this dish.

Options for Substitutions

This breakfast bake is pretty forgiving when it comes to swaps, so feel free to work with what you have:

• Ham: Cooked bacon, sausage, or turkey work great here. You can also use leftover rotisserie chicken if that’s what you have on hand. Just make sure whatever meat you use is already cooked.
• Cheddar cheese: Switch it up with Monterey Jack, Colby, Swiss, or Gruyere. You can also do a mix of cheeses – just keep the total amount the same.
• Heavy whipping cream: Half-and-half works in a pinch, though your bake will be slightly less rich. For a dairy-free option, try full-fat coconut cream.
• Sour cream: Greek yogurt or cream cheese can step in here. If using cream cheese, let it soften first so it mixes in smoothly.
• Bell peppers and onions: Use whatever color peppers you prefer, or swap in mushrooms, spinach, or tomatoes. Just keep the total veggie amount about the same.
• Dry mustard: Regular prepared mustard works too – use about 1 teaspoon and reduce the liquid slightly if your bake seems too wet.

Watch Out for These Mistakes While Baking

The biggest mistake with this breakfast bake is skipping the step of sautéing your peppers and onions first – raw vegetables release water as they cook, which can make your casserole watery and prevent it from setting properly.

Another common error is overbaking, which turns the eggs rubbery and dry, so pull the dish from the oven when the center still has a slight jiggle (around 160°F on an instant-read thermometer) since it will continue cooking as it rests.

To get an even distribution of ham and cheese throughout, layer half the ham and 1 cup of cheese in the middle of the casserole before pouring in the egg mixture, then top with the remaining cheese during the last 10 minutes of baking.

Finally, resist cutting into it immediately – letting the bake rest for 10 minutes allows it to firm up and makes slicing much cleaner.

What to Serve With Ham and Cheese Breakfast Bake?

This breakfast bake is pretty filling on its own, but I love serving it with some fresh fruit on the side like berries or sliced melon to balance out the richness. A simple arugula or spinach salad with a light vinaigrette also works great if you want something green on your plate. For a heartier breakfast spread, you can add some crispy bacon strips or breakfast sausage links alongside it. If you’re feeding a crowd for brunch, consider setting out some sliced avocado, salsa, or hot sauce so everyone can customize their plate however they like.

Storage Instructions

Store: This breakfast bake is perfect for meal prep! Once it’s cooled down, cover the dish tightly with plastic wrap or transfer portions to airtight containers. It’ll stay fresh in the fridge for up to 4 days, making your morning routine so much easier.

Freeze: You can definitely freeze this for later. Cut it into individual portions and wrap each piece in plastic wrap, then place them all in a freezer-safe container or bag. They’ll keep for up to 2 months, which is great when you want a quick breakfast ready to go.

Reheat: Warm up individual portions in the microwave for about 1-2 minutes, or pop them in a 350°F oven for 10-15 minutes until heated through. If reheating from frozen, add a few extra minutes or let it thaw in the fridge overnight first.

Estimated Nutrition

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

• Calories: 2200-2400
• Protein: 140-155 g
• Fat: 170-185 g
• Carbohydrates: 20-28 g

Ingredients

For the bake:

• 2 cups shredded cheddar cheese (I use Cabot sharp cheddar)
• 1/2 tsp salt
• 2 tbsp onion (finely diced)
• 1/2 tsp smoked paprika
• 1 tsp dry mustard
• avocado oil spray
• 1 tbsp butter (I use Kerrygold unsalted)
• 1/2 tsp black pepper
• 1/2 cup heavy whipping cream (makes it extra creamy)
• 1/4 cup sour cream
• 2 tbsp green peppers (finely diced)
• 14 eggs (room temperature preferred)
• 2 cups diced cooked ham
• 2 tbsp red peppers (finely diced)

For topping:

• 1/2 cup shredded cheddar cheese
• sour cream for serving (optional, adds richness)

Step 1: Prepare the Mise en Place and Preheat

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

Start by preheating your oven to 350°F.

While it heats, finely dice the onion, green peppers, and red peppers, keeping them separate so you can add them at the right time.

Crack all 14 eggs into a large mixing bowl and set aside.

This mise en place approach ensures you’re not scrambling for ingredients once you start building the bake.

I like to have everything prepped before I start cooking—it keeps the process smooth and stress-free.

Step 2: Sauté the Vegetables and Build Flavor

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

Spray a 9×13 inch baking dish lightly with avocado oil.

In a skillet over medium heat, melt the butter and add the diced onion and peppers together.

Sauté for 4-5 minutes, stirring occasionally, until the vegetables are softened and the onion becomes translucent.

This short cooking time softens the vegetables just enough while keeping them from becoming too tender in the long bake ahead.

The butter also carries the flavor beautifully into the final dish.

Step 3: Create 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

To the bowl with the cracked eggs, add the heavy whipping cream, sour cream, dry mustard, salt, smoked paprika, and black pepper.

Whisk vigorously for about 1-2 minutes until the mixture is well combined and slightly frothy—this incorporates air and helps create a lighter, more custard-like texture in the bake.

The spices distribute evenly when whisked into the wet base rather than added later.

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 shredded cheddar cheese to the egg custard mixture from Step 3.

Stir gently but thoroughly until everything is evenly distributed—you want the ham and cheese distributed throughout so each bite has all the flavors.

I prefer to use sharp cheddar because it has more depth and doesn’t get lost in the rich, creamy custard.

Step 5: Assemble and Top the Bake

• combined mixture from Step 4
• 1/2 cup shredded cheddar cheese
• prepared baking dish from Step 2

Pour the combined egg and filling mixture into the prepared baking dish from Step 2, distributing it evenly.

Sprinkle the remaining 1/2 cup of shredded cheddar cheese over the top as a finishing layer—this creates a beautiful golden crust as it bakes.

The cheese on top acts as both a flavor layer and a visual indicator of doneness.

Step 6: Bake Until Set and Golden

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

The bake is done when the center is set but still has a slight jiggle when you gently shake the dish—it should not be completely firm or it will be dry.

The top should be golden brown and the edges slightly pulled away from the sides of the dish.

Let it rest for 5 minutes before serving, which allows the custard to firm up slightly and makes it easier to cut into clean portions.

Step 7: Serve and Finish

• sour cream for serving

Slice the bake into portions and serve warm.

Top each serving with an extra dollop of sour cream if desired for added richness and tang.

This breakfast bake holds well and makes excellent leftovers—simply reheat gently in a 325°F oven or microwave.

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 2300 kcal

Ingredients

  

For the bake:

• 2 cups shredded cheddar cheese (I use Cabot sharp cheddar)
• 1/2 tsp salt
• 2 tbsp onion (finely diced)
• 1/2 tsp smoked paprika
• 1 tsp dry mustard
• avocado oil spray
• 1 tbsp butter (I use Kerrygold unsalted)
• 1/2 tsp black pepper
• 1/2 cup heavy whipping cream (makes it extra creamy)
• 1/4 cup sour cream
• 2 tbsp green peppers (finely diced)
• 14 eggs (room temperature preferred)
• 2 cups diced cooked ham
• 2 tbsp red peppers (finely diced)

For topping:

• 1/2 cup shredded cheddar cheese
• sour cream for serving (optional, adds richness)

Instructions

 

• Start by preheating your oven to 350°F. While it heats, finely dice the onion, green peppers, and red peppers, keeping them separate so you can add them at the right time. Crack all 14 eggs into a large mixing bowl and set aside. This mise en place approach ensures you're not scrambling for ingredients once you start building the bake. I like to have everything prepped before I start cooking—it keeps the process smooth and stress-free.
• Spray a 9x13 inch baking dish lightly with avocado oil. In a skillet over medium heat, melt the butter and add the diced onion and peppers together. Sauté for 4-5 minutes, stirring occasionally, until the vegetables are softened and the onion becomes translucent. This short cooking time softens the vegetables just enough while keeping them from becoming too tender in the long bake ahead. The butter also carries the flavor beautifully into the final dish.
• To the bowl with the cracked eggs, add the heavy whipping cream, sour cream, dry mustard, salt, smoked paprika, and black pepper. Whisk vigorously for about 1-2 minutes until the mixture is well combined and slightly frothy—this incorporates air and helps create a lighter, more custard-like texture in the bake. The spices distribute evenly when whisked into the wet base rather than added later.
• Add the sautéed vegetables from Step 2, the diced cooked ham, and 2 cups of shredded cheddar cheese to the egg custard mixture from Step 3. Stir gently but thoroughly until everything is evenly distributed—you want the ham and cheese distributed throughout so each bite has all the flavors. I prefer to use sharp cheddar because it has more depth and doesn't get lost in the rich, creamy custard.
• Pour the combined egg and filling mixture into the prepared baking dish from Step 2, distributing it evenly. Sprinkle the remaining 1/2 cup of shredded cheddar cheese over the top as a finishing layer—this creates a beautiful golden crust as it bakes. The cheese on top acts as both a flavor layer and a visual indicator of doneness.
• Slide the baking dish into the preheated 350°F oven and bake for 50-60 minutes. The bake is done when the center is set but still has a slight jiggle when you gently shake the dish—it should not be completely firm or it will be dry. The top should be golden brown and the edges slightly pulled away from the sides of the dish. Let it rest for 5 minutes before serving, which allows the custard to firm up slightly and makes it easier to cut into clean portions.
• Slice the bake into portions and serve warm. Top each serving with an extra dollop of sour cream if desired for added richness and tang. This breakfast bake holds well and makes excellent leftovers—simply reheat gently in a 325°F oven or microwave.