Everything Bagel Breakfast Casserole

Get ready to transform your weekend brunch game with this incredible Everything Bagel Breakfast Casserole that’s about to become your new obsession!

Picture this: tender, day-old everything bagels soaking up a rich, creamy custard base while crispy bacon, colorful bell peppers, and juicy cherry tomatoes create the perfect flavor symphony.

The star of the show?

Those gorgeous pockets of melted cream cheese that create little bursts of indulgence in every single bite.

This isn’t just breakfast – it’s a celebration on a plate that’ll have your family racing to the kitchen table.

What makes this casserole absolutely irresistible is how it captures all the beloved flavors of a loaded everything bagel sandwich but transforms them into something even more spectacular.

The everything bagel seasoning adds that signature savory crunch, while the combination of whole milk and eggs creates a custard-like texture that’s pure comfort food magic.

Plus, you can assemble this beauty the night before, which means you get to be the hero of breakfast without the early morning stress.

The aroma alone will have your neighbors wondering what amazing thing is happening in your kitchen!

Ingredients

For the Base

• 3 day-old everything bagels, cut into bite-size pieces (about 6 cups)
• 1 bell pepper, chopped
• 3 /4 cup (113g) quartered cherry tomatoes (or chopped regular tomato)
• 6 slices cooked bacon, chopped

For the Custard

• 9 large eggs
• 1 and 1/2 cups whole milk
• 1 and 1/2 cups shredded cheese
• 1 /2 teaspoon ground mustard
• 1 /4 teaspoon salt
• 1 /8 teaspoon freshly ground black pepper

For the Topping

• 6 ounces (170g) full-fat brick cream cheese, cut into bite-size pieces

Instructions

Instructions

1. 1 Preheat your oven to 375°F (191°C). Generously grease a 9×13-inch baking pan or similar size (about 3-quart) casserole dish with butter or cooking spray. This generous greasing is crucial for easy serving and prevents the custard from sticking to the sides during the long baking process.
2. 2 Layer the bagel pieces evenly across the bottom of your prepared dish, creating a sturdy foundation. Distribute the chopped bell pepper, quartered cherry tomatoes, and bacon pieces over the bagel layer, ensuring even distribution so every serving gets a perfect balance of flavors. The vegetables will release moisture during baking, which helps create the creamy texture.
3. 3 In a large mixing bowl, whisk together the eggs, whole milk, shredded cheese, ground mustard, salt, and freshly ground black pepper until completely combined. The mixture should be smooth and well-integrated – this custard base is what transforms your bagel pieces into a cohesive, restaurant-quality casserole. Pour this mixture evenly over the bagel and vegetable layers, making sure to reach all corners of the dish.
4. 4 Distribute the bite-size cream cheese pieces evenly across the top of the casserole. These will create pockets of rich, tangy creaminess as they melt during baking. Sprinkle with everything bagel seasoning if you want that extra burst of savory flavor and visual appeal.
5. 5 Bake for 40-50 minutes, checking at the 40-minute mark for doneness. The casserole is perfectly cooked when the center is completely set (no jiggling when gently shaken) and the edges are beautifully golden brown. If the top starts browning too quickly, tent loosely with aluminum foil for the remaining baking time.
6. 6 Remove from the oven and allow to cool for 10 minutes before serving. This resting time is essential – it allows the custard to finish setting and makes slicing much cleaner. Top with fresh scallions if desired, then slice and serve while still warm.
7. 7 Cover any leftover casserole tightly with plastic wrap or aluminum foil and refrigerate for up to 1 week. Reheat individual portions in the microwave for 30-45 seconds or warm larger portions in a 300°F (149°C) oven until heated through.

Recommended Equipment and Kitchen Tools

Recommended Tools (for best results):

• 9×13-inch baking pan or 3-quart casserole dish – A quality baking dish with straight sides ensures even cooking and easy serving
• Large mixing bowls – Essential for whisking the custard base thoroughly and preventing lumps
• Wire whisk – Creates the smoothest custard texture by incorporating air and breaking up any egg proteins
• Sharp chef’s knife – Makes quick work of chopping vegetables and cutting day-old bagels into uniform pieces

Helpful Upgrades:

• Kitchen scale – For precise measurements, especially when portioning the cream cheese and cherry tomatoes
• Silicone spatula – Perfect for scraping every bit of custard from your mixing bowl and ensuring nothing goes to waste
• Aluminum foil – Handy for tenting the casserole if the top browns too quickly during baking
• Instant-read thermometer – Professional bakers use this to check that the center reaches 160°F (71°C) for food safety

Nice-to-Have Options:

• Bench scraper – Makes transferring chopped vegetables from cutting board to casserole dish effortless
• Parchment paper – Line your baking dish for even easier cleanup, though greasing works perfectly well
• Storage containers – Glass containers with tight-fitting lids keep leftovers fresh and make reheating simple

Recipe Variations and Dietary Modifications

Gluten-Free Adaptation:

• Replace everything bagels with 6 cups cubed gluten-free bread or gluten-free bagels
• Add an extra 1/4 cup milk as gluten-free bread absorbs liquid differently
• Increase baking time by 5-10 minutes as gluten-free versions may need longer to set completely
• Check that your everything bagel seasoning is certified gluten-free

Dairy-Free Modifications:

• Substitute unsweetened oat milk or almond milk for whole milk (use same amount)
• Replace shredded cheese with dairy-free cheese shreds or nutritional yeast for cheesy flavor
• Use dairy-free cream cheese or omit entirely and add extra vegetables for texture
• The texture will be slightly less rich but still deliciously satisfying

Vegetarian Version:

• Replace bacon with vegetarian bacon strips or sautéed mushrooms for umami depth
• Add diced avocado after baking for healthy fats and creamy texture
• Include sun-dried tomatoes for concentrated flavor without meat
• Caramelized onions add sweetness and complexity

Flavor Variations:

• Mediterranean style: Add olives, feta cheese, and fresh herbs like oregano or basil
• Southwestern twist: Include diced jalapeños, pepper jack cheese, and cilantro
• Garden vegetable: Load up with zucchini, spinach, and roasted red peppers
• Smoked salmon version: Replace bacon with flaked smoked salmon and add capers

Nutritional Information and Health Benefits

Key Nutritional Highlights:
This hearty breakfast casserole provides approximately 285 calories per serving when cut into 12 portions. Each serving delivers a substantial 18 grams of protein from the eggs, cheese, and bacon, making it an excellent choice for sustained morning energy. The combination of whole milk and eggs provides complete proteins containing all essential amino acids your body needs. With approximately 8 grams of carbohydrates per serving, this casserole offers steady energy without the blood sugar spikes associated with sugary breakfast options.

Health Benefits of Main Ingredients:
The eggs in this recipe are nutritional powerhouses, providing high-quality protein, choline for brain health, and lutein for eye health. Bell peppers contribute significant vitamin C – even more than citrus fruits – along with antioxidants that support immune function. Cherry tomatoes offer lycopene, a powerful antioxidant that becomes more bioavailable when cooked, plus folate and potassium. The whole milk provides calcium for bone health and vitamin D for immune support, while the everything bagel seasoning adds beneficial compounds from sesame seeds, including healthy fats and lignans.

Dietary Considerations:
This recipe contains gluten (from bagels), dairy (milk, cheese, cream cheese), and eggs, making it unsuitable for those with these specific allergies. However, it’s naturally nut-free and can easily accommodate various dietary needs with simple substitutions. The high protein content makes it particularly satisfying for active individuals or those following higher-protein eating patterns. Consider pairing with fresh fruit to add fiber and additional vitamins for a more complete nutritional profile.

Smart Swaps and Ingredient Substitutions

Common Substitutions:

• Everything bagels → Plain bagels plus 2 tablespoons everything seasoning mixed into custard
• Bell pepper → Zucchini, mushrooms, or roasted red peppers (same amount)
• Cherry tomatoes → Regular tomatoes diced or sun-dried tomatoes (use half the amount)
• Bacon → Turkey bacon, ham, or breakfast sausage (cooked and chopped)
• Whole milk → Half-and-half for richer texture or 2% milk for lighter version

Budget-Friendly Swaps:

• Day-old everything bagels → Stale bread cubes plus everything seasoning
• Cream cheese → Extra shredded cheese or cottage cheese for similar creaminess
• Fresh herbs for garnish → Dried herbs mixed into the custard base
• Organic eggs → Conventional eggs work perfectly for this recipe

Pantry Emergency Substitutions:

• Fresh bell pepper → 1/2 cup frozen bell pepper strips (thawed and drained)
• Cherry tomatoes → 1/2 cup canned diced tomatoes (drained well)
• Everything bagel seasoning → Mix sesame seeds, poppy seeds, garlic powder, onion powder, and salt
• Ground mustard → Dijon mustard (use same amount)

Pro Tips for Substitutions:

• When using frozen vegetables, thaw completely and pat dry to prevent excess moisture
• If substituting different bread types, adjust milk quantity based on how much the bread absorbs
• Store leftover everything bagel seasoning in an airtight container for up to 6 months

Make It Diabetes-Friendly

Carb Reduction Strategies:

• Replace 3 everything bagels with 2 bagels plus 2 cups cauliflower florets to reduce carbs by approximately 30 grams
• Use unsweetened almond milk instead of whole milk to save 12 grams carbs per serving
• Increase non-starchy vegetables like bell peppers, tomatoes, and add spinach or mushrooms for volume without carbs
• Consider low-carb bagel alternatives or cloud bread if available in your area

Protein Enhancement:

• Add extra eggs (up to 12 total) to increase protein and satiety without adding carbs
• Include turkey sausage or lean ham for additional protein that helps stabilize blood sugar
• Greek yogurt (2-3 tablespoons) mixed into custard adds protein and probiotics
• Cottage cheese can partially replace cream cheese for higher protein content

Portion & Timing Tips:

• Cut into 16 smaller portions instead of 12 for better portion control
• Estimated carbs per smaller serving: approximately 6-8 grams
• Pair with avocado slices or nuts for healthy fats that slow glucose absorption
• Best timing: Serve as part of a balanced breakfast with protein and healthy fats

Blood Sugar Management:

• The high protein content (18g per serving) helps minimize blood sugar spikes
• Fiber from vegetables slows carbohydrate absorption
• Consider adding chia seeds or ground flaxseed for additional fiber and omega-3s

Perfect Pairing Suggestions

Beverage Pairings:
A crisp Prosecco or Champagne beautifully complements the rich, savory flavors while cutting through the cream cheese richness. For beer lovers, a light wheat beer or pilsner provides refreshing contrast without overwhelming the delicate egg custard. Fresh orange juice mixed with sparkling water creates a bright, non-alcoholic option that enhances the everything bagel flavors. Coffee with a splash of cream is the classic breakfast pairing, while Earl Grey tea offers a sophisticated alternative with bergamot notes that complement the herbs in everything seasoning.

Side Dish Recommendations:
Fresh fruit salad with berries and citrus provides acidic brightness that cuts through the rich casserole perfectly. Arugula salad with lemon vinaigrette adds peppery freshness and helps balance the meal’s richness. Roasted asparagus or sautéed spinach contribute color, nutrients, and a pleasant textural contrast. Hash browns or breakfast potatoes turn this into an ultimate weekend brunch spread, while fresh berries with mint offer a light, refreshing finish.

Complete Meal Ideas:
Start with smoked salmon and bagel bites as an appetizer to continue the bagel theme elegantly. Follow the casserole with lemon scones or fresh pastries for a complete brunch buffet. For entertaining, add bacon-wrapped asparagus and fruit kabobs to create a stunning spread. Mimosa bar with various fruit juices lets guests customize their drinks while you enjoy stress-free hosting.

Occasion Suggestions:
This casserole shines at weekend brunches, holiday mornings, and overnight guest breakfasts. Perfect for Mother’s Day or Easter brunch when you want something special but manageable. Potluck breakfasts and office gatherings benefit from its make-ahead convenience and crowd-pleasing appeal. The elegant presentation makes it suitable for bridal showers or baby showers when served alongside fresh fruit and pastries.

Pro Tips and Troubleshooting

Professional Techniques:
Use day-old bagels specifically because fresh bagels won’t absorb the custard properly and may result in a soggy texture. Room temperature eggs incorporate more easily into the custard, preventing lumps and ensuring even cooking. Strain your custard mixture through a fine-mesh sieve if you notice any lumps from the eggs or cheese. Rest the assembled casserole for 15 minutes before baking if making fresh – this allows the bagels to begin absorbing the liquid for more even cooking.

Common Mistake Prevention:
Never skip the cooling period – cutting too early results in a messy, runny presentation that doesn’t hold its shape. Don’t overbake as the eggs will become rubbery and the texture will suffer; the center should be just set, not firm. Avoid using fresh bagels as they won’t absorb enough liquid and will create uneven texture. Don’t skip greasing the pan thoroughly, as the egg proteins will stick stubbornly to ungreased surfaces.

Storage and Reheating:
Refrigerate leftovers within 2 hours of baking for food safety. Individual portions reheat best in the microwave for 45-60 seconds, while larger portions should go in a 300°F (149°C) oven covered with foil. Freezing works well for up to 3 months – wrap individual portions in plastic wrap, then foil. Thaw overnight in refrigerator before reheating for best results.

Make-Ahead Strategies:
Assemble completely the night before, cover tightly, and refrigerate. Add 10-15 minutes to baking time when starting from cold. Prep ingredients separately up to 2 days ahead – store chopped vegetables, cooked bacon, and custard mixture separately, then combine on baking day.

This Everything Bagel Breakfast Casserole represents everything wonderful about weekend mornings – the comfort of sleeping in, the joy of sharing delicious food with people you love, and the satisfaction of creating something truly special without spending hours in the kitchen. Whether you’re hosting a crowd or treating your family to something extraordinary, this recipe delivers restaurant-quality results with home-kitchen simplicity. The combination of familiar bagel shop flavors transformed into an elegant casserole format makes every bite a delightful surprise that’ll have everyone asking for the recipe!