Easy & Healthy Whole Wheat Breakfast Quesadillas

Healthy Bacon Egg Cheese Breakfast Quesadillas: Your Ultimate Whole-Grain Recipe

Discover how to create the most satisfying and wholesome Bacon Egg Cheese Breakfast Quesadillas right in your own kitchen! This recipe takes a beloved breakfast classic and elevates it with healthier ingredients, focusing on whole-grain tortillas, quality proteins, and fresh flavors. Whether you’re seeking a quick weekday meal or a delightful weekend brunch, these quesadillas are incredibly versatile, easy to customize, and guaranteed to become a family favorite. We love serving them with a dollop of sour cream (or Mexican crema), a spoonful of vibrant salsa, or a dash of your favorite hot sauce for an extra kick. Plus, they’re perfect for utilizing leftover cheese, veggies, or meat, transforming them into delicious “egg cheese sandwiches” packed with extra protein and nutrients.

healthy breakfast quesadillas using whole wheat flour tortillas, bacon with no nitrates, free-range eggs, and freshly grated cheese served with homemade salsa and Crema

A classic breakfast quesadilla recipe is an indispensable part of any home cook’s repertoire. This particular version takes the traditional concept and elevates it by using pan-fried crispy bacon and fluffy scrambled eggs, all made from scratch for superior flavor and texture. If you’re looking for a quicker assembly, consider our Mini Breakfast Quesadillas, which ingeniously use whole fried eggs and convenient bacon bits, perfect for busy mornings. But for that truly comforting, homemade experience, this recipe is your go-to guide.

Crafting Your Healthy Breakfast Quesadilla

Our philosophy for breakfast quesadillas leans towards a slightly healthier approach without compromising on taste. The foundation of this recipe lies in the use of whole grains, specifically through homemade whole wheat tortillas. These provide a richer, nuttier flavor and a significant boost in fiber compared to their refined counterparts. If pork isn’t part of your diet, turkey bacon offers a leaner, yet equally delicious, protein alternative that pairs wonderfully with the eggs and cheese.

While I wholeheartedly endorse the joy of baking bread and crafting homemade flour tortillas, convenience sometimes calls for store-bought options. When selecting tortillas, prioritize brands that use wholesome ingredients. Look for options with minimal additives and a high whole-grain content. The tortillas from Azure Standard, for instance, are an excellent choice that meets these criteria, ensuring your breakfast quesadillas are both convenient and nutritious.

Achieving that coveted super-crisp tortilla exterior is key to a truly great quesadilla. Cooking them in a bit of fat helps immensely. I often opt for the flavorful bacon grease rendered from nitrate-free bacon, which adds an incredible depth of savory flavor. However, if you prefer a lighter option, avocado oil is a fantastic substitute, offering a neutral taste and high smoke point. While a little fat aids in crisping, you can reduce oil usage further by baking your quesadillas in the oven or using an air fryer for a similarly crispy finish with less added oil.

The Irresistible Appeal of Breakfast Quesadillas

Breakfast Quesadillas are not only incredibly delicious but also remarkably simple to prepare, especially when you have leftover scrambled eggs or pre-cooked bacon on hand. They offer a brilliant way to create satisfying, Mexican-inspired flat cheese sandwiches, allowing for endless customization.

Imagine the possibilities: finely diced bell peppers, a pinch of dried red chile (like cayenne pepper) for warmth, savory chorizo or breakfast sausage, spoonfuls of fresh salsa, or even hearty black beans for an extra protein punch. These aren’t just for breakfast; they make fantastic quick lunches or light dinners too. Their versatility truly shines as you can easily tailor them to your preference, from plain eggs and cheese to a vibrant explosion of Southwest flavors. This adaptability also extends to your choice of breakfast quesadilla sauce and side toppings, like creamy slices of avocado, making each meal a unique experience.

bacon, egg, cheese breakfast quesadilla with whole wheat tortillas

Mise en Place: Gathering Your Essentials

Equipment:

  • Large non-stick skillet (or cast-iron): A good quality skillet is crucial for even cooking and achieving that perfect golden-brown crispness. Cast iron offers excellent heat retention for consistent results, while non-stick makes flipping and cleanup a breeze.
  • Turner: Essential for safely flipping your quesadillas. Use a metal turner for cast iron to get under the crispy edges, or a flexible silicone turner for non-stick pans to protect the surface from scratches.
  • Mixing bowl: A medium-sized bowl is perfect for whisking eggs and ensuring they are well-seasoned and aerated for fluffy scrambled eggs.

Watch How to Make these Quesadillas!

Key Ingredients for Delicious Egg Quesadillas:

Our breakfast quesadillas feature a simple yet powerful combination of ingredients. For those craving extra Tex-Mex flair, consider adding diced jalapeños and sautéed onions and bell peppers to the mix.

  • Bacon: Opt for high-quality, smoked sliced bacon, specifically varieties labeled “no nitrate added.” Many brands, including those found at stores like Aldi (“never any” brand), offer this healthier option, ensuring you’re avoiding unnecessary preservatives while enjoying rich, savory flavor.
  • Eggs: The quality of your eggs truly makes a difference. Look for Grade AA eggs, which signify the highest quality. We’re fortunate to use eggs from our own backyard chickens, but for store-bought options, “Happy Eggs” or other free-range, pasture-raised brands are excellent choices for both taste and ethical sourcing.
  • Cheese: The secret to a gooey, satisfying quesadilla lies in the cheese. A Mexican cheese blend is a convenient option, but for superior melt and flavor, we recommend grating your own. Blocks of Cheddar, Mozzarella, Monterey Jack, or Colby cheese are all fantastic choices that melt beautifully and allow you to create your preferred custom blend.
  • Tortillas: Eight-inch flour tortillas are the ideal size for breakfast quesadillas. They hold the fillings securely without being too unwieldy, making them easy to fold, cook, and eat. Larger tortillas can sometimes lead to fillings spilling out when cut into wedges.

Note: If whole wheat tortillas are difficult to find, or if you’re looking for a lower-carb alternative, consider using options like these Mission Carb Balance tortillas.

ingredients for breakfast quesadillas (whole wheat flour tortillas, bacon with no nitrates, milk, free-range-eggs, eggs, block of Monterey Jack and Colby cheese, avocado oil if bacon grease is omitted)

How To Assemble and Cook Your Perfect Breakfast Quesadilla:

This streamlined breakfast quesadilla recipe is designed for maximum flavor with minimal cleanup, largely made in a single pan! For your convenience, a printable version of these instructions can be found in the recipe card further down this page.

Alternative: For Sheet Pan (Oven-Baked) Breakfast Quesadillas: Preheat your oven to 350°F (176°C). Arrange four tortillas evenly spaced on a baking sheet. Generously scatter cheese over two of the tortillas, then add a layer of scrambled eggs and crispy bacon. Top with more cheese to act as a “glue,” and finally, place the remaining two tortillas on top. Drizzle lightly with oil or brush with melted butter. Bake for 12-15 minutes, or until the tortillas are golden brown and the cheese is melted and bubbly.

  1. Brown the bacon: In a large, preheated skillet (preferably cast-iron for superior crisping), fry your bacon slices until they reach your desired level of crispness. You can chop the bacon into bite-sized pieces before or after cooking, depending on your preference. Once cooked, transfer the bacon to a plate lined with paper towels to drain excess fat. Reserve 1-2 tablespoons of the flavorful bacon grease in the skillet for cooking the eggs and quesadillas.
  2. Prep the eggs: While the bacon cooks, crack your eggs into a medium mixing bowl. Add the milk, a pinch of salt, and a dash of black pepper. Whisk vigorously until the yolks and whites are fully combined and slightly frothy. This aeration helps create wonderfully fluffy scrambled eggs.
  3. Cook the eggs: Pour the whisked egg mixture into the same skillet used for the bacon, utilizing the reserved bacon grease for added flavor. Cook over medium heat, stirring occasionally with a spatula, until the eggs are scrambled to your liking – soft, fluffy, and thoroughly cooked. Remove the scrambled eggs from the pan using a slotted spoon to drain any remaining grease, and set aside. Carefully wipe the skillet clean with a paper towel, leaving just a thin film of fat for the quesadillas, or add fresh oil if preferred.
  4. Assemble the quesadilla: This is where the magic happens! Lay three 8-inch flour tortillas flat on a clean countertop. On one half of each tortilla, evenly distribute a layer of shredded cheese. Follow with a generous portion of scrambled eggs and crispy bacon pieces. Crucially, add another layer of cheese on top of the eggs and bacon. This top layer of cheese acts as the “glue” that holds the two tortillas together as it melts. Finally, place the remaining three tortillas on top of the filled halves, creating three double-decker quesadillas.
  5. Cook until Crisp: Return the clean skillet to medium-high heat. Add about 2 tablespoons of the reserved bacon grease (or avocado oil). Once shimmering, carefully place one or two assembled quesadillas into the hot skillet, ensuring they fit comfortably without overcrowding. Cook for 3-5 minutes per side, or until each side is beautifully golden-brown and crispy, and the internal cheese is gloriously melted and oozing. Repeat with the remaining quesadillas, adding more fat to the pan as needed.
  6. Cut into Wedges: Once cooked, transfer the quesadillas to a cutting board. Using a sharp knife or a pizza cutter, slice each double-decker quesadilla into quarters, creating easy-to-handle wedges.

Pro Tip for Little Ones: For half-moon shaped quesadillas, simply fold the tortilla in half over the fillings before cooking. Cutting them into smaller wedges makes them easier for little hands to grab and enjoy!

Pro Chef Tip

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The Cheese-to-Filling Ratio: When arranging your egg quesadillas, remember that cheese is your best friend for both flavor and structure. Let the cheese predominate, ensuring it forms a good “glue” between the tortillas and provides that irresistible gooey texture. Go slightly lighter on the eggs and meat to prevent the quesadilla from becoming too bulky and difficult to hold together, especially when sliced.

Jump to Tips

Delicious Variations to Try:

Elevate your breakfast quesadillas with these mouth-watering additions:

  • Spicy Kick: For those who love a bit of heat, finely dice and deseed one fresh jalapeño and mix it into the eggs, or simply sprinkle some red pepper chili flakes over the filling before cooking.
  • Tex-Mex Flair: Sauté finely diced bell peppers (any color!) and onions in a touch of bacon grease or oil until softened and slightly caramelized before adding them to your quesadilla filling. This adds incredible depth of flavor.
  • Creamy Avocados: Top your finished quesadillas with fresh slices of ripe avocado or a dollop of creamy guacamole for a rich, healthy fat and a cooling counterpoint to any spice.
  • Hearty Protein Boost: Swap or supplement bacon with browned breakfast sausage or spicy chorizo for a different flavor profile. Make sure to drain any excess grease before adding to the quesadillas.
  • Nutritious Beans: For extra protein and fiber, drain and rinse a can of your favorite beans (such as black beans or pinto beans) and sprinkle them over the cheese and egg mixture.
  • My Favorite Variation: While the basic bacon, egg, and cheese version is a hit with my kids, I adore adding more vegetables. After cooking 4-6 slices of bacon, remove them and sauté one diced onion, one diced bell pepper, and a tablespoon of pickled jalapeño slices in the remaining bacon grease until tender. Then, mix in one cubed avocado. Assemble the quesadillas as instructed; this variation is bursting with flavor!

The Best Breakfast Quesadilla Sauces:

No quesadilla is complete without the perfect dipping sauce! Here are our all-time favorites:

  • Crema (or Sour Cream): A classic choice. For a smoother, more dip-friendly consistency, whisk a splash of milk into thick sour cream or traditional Mexican crema until it reaches your desired creaminess.
  • Pico de Gallo: This fresh salsa fresca, bursting with ripe tomatoes, onions, cilantro, and jalapeño, offers a vibrant, zesty counterpoint to the rich quesadilla. Its fresh ingredients brighten every bite.
  • Salsa: Whether homemade or store-bought, salsa is a fantastic condiment. Jarred or canned salsa is perfect for enjoying the flavors of tomatoes even when they’re out of season. It’s a convenient, flavorful addition that you can always have on hand. Don’t miss my favorite salsa recipe for canning!

Make-Ahead & Freezer-Friendly Breakfast Quesadillas:

Are you not a morning person but still crave a delicious, homemade breakfast? These quesadillas are perfect for meal prepping! You can easily prepare components ahead of time to make mornings a breeze.

Prep Ahead Tips:

  • Scrambled Eggs: Cook a larger batch of scrambled eggs and store them in an airtight container in the refrigerator for up to 3-4 days.
  • Oven-Baked Bacon: Bake a big batch of bacon in the oven until crispy. Once cooled, store it in the fridge for up to a week, or freeze it for longer-term storage (bacon freezes exceptionally well!).

With pre-cooked eggs and bacon, assembling your quesadillas in the morning takes less than 10 minutes!

Freezing Assembled Quesadillas: For the ultimate convenience, you can freeze fully assembled breakfast quesadillas, much like a friend who freezes breakfast burritos. The concept is essentially the same. Simply assemble the quesadillas in a half-moon shape (or whole, if preferred) and flash freeze them on a baking sheet until solid. Once frozen, transfer them to a freezer-safe bag or airtight container. They will keep well in the freezer for up to 3 months, ready for a grab-and-go breakfast solution.

To Reheat Frozen Quesadillas:

  1. Thaw: For best results, thaw the frozen quesadillas overnight in the refrigerator.
  2. Bake: In the morning, arrange the thawed quesadillas on a lightly greased baking pan. Drizzle or lightly brush the tops with a little oil or melted butter to help with crisping.
  3. Cook: Bake in a preheated oven at 400°F (200°C) for approximately 15 minutes, or until they are heated through, golden, and wonderfully crisp.
  4. Air Fryer: Alternatively, an air fryer can reheat quesadillas from thawed or even frozen (with slightly longer cooking time) to crispy perfection. Cook at 350°F (175°C) for 5-8 minutes (thawed) or 10-15 minutes (frozen), flipping halfway, until crisp and hot.

Q&A: Common Questions About Breakfast Quesadillas

How do Breakfast Quesadillas Taste?

Our breakfast quesadillas offer a delightful combination of textures and flavors. The whole-grain tortillas are soft yet crisp after cooking, enveloping a filling of fluffy, moist scrambled eggs, savory, smoky bacon, and gloriously gooey melted cheese. For those who enjoy more adventurous flavors, adding hot peppers, sautéed onions, and bell peppers can introduce a vibrant Southwest kick, while a dollop of salsa adds a fresh tang.

What Size Tortillas are Best for Breakfast Quesadillas?

For optimal results and ease of eating, egg breakfast quesadillas are best made with smaller six- to eight-inch tortillas. This size ensures a good balance between the tortilla and the filling. Using larger tortillas can make the quesadillas unwieldy, and when cut into wedges, the larger sections tend to be weaker, increasing the likelihood of the delicious scrambled egg filling falling out. The 8-inch size allows for a sturdy, satisfying wedge every time.

 

Can I make these vegetarian?

Absolutely! These breakfast quesadillas are incredibly versatile. Simply omit the bacon and load up on your favorite vegetables like bell peppers, onions, spinach, mushrooms, or even some black beans for extra protein and fiber. The core combination of eggs, cheese, and whole-grain tortillas provides a delicious foundation for a satisfying vegetarian meal.

What’s the best way to get crispy tortillas?

To achieve perfectly crispy tortillas, ensure your skillet is adequately heated over medium-high heat before adding the quesadillas. Using a small amount of fat (like bacon grease, butter, or avocado oil) is essential. Don’t overcrowd the pan, as this can steam the tortillas instead of crisping them. Cook each side for a few minutes until golden brown and slightly firm. If you prefer, an air fryer or oven can also yield crispy results with less oil.

Expert Breakfast Quesadilla Tips:

  1. Repurpose Leftovers: Don’t let anything go to waste! These quesadillas are fantastic for using up leftover proteins like shredded Carnitas, salsa chicken, deli ham, or even store-bought rotisserie chicken. Simply shred or dice and add to your filling.
  2. Outdoor Cooking Adventure: Planning a camping trip or an outdoor gathering? These quesadillas cook beautifully on a Blackstone griddle or any flat-top grill, making them an excellent choice for al fresco dining.
  3. Smart Meal Prep: Take advantage of the make-ahead and freezing options discussed above. Preparing a batch of these quesadillas in advance ensures you always have a quick, healthy, and satisfying breakfast at your fingertips, even on the busiest mornings.
  4. Vegetarian-Friendly Option: Hosting vegetarian guests or simply looking for a meatless meal? Easily adapt this recipe by skipping the bacon and instead adding a variety of sautéed vegetables, beans, or even a plant-based sausage for a equally delicious experience.
  5. Choose Quality Fats: When cooking, consider using animal fats (like the rendered bacon grease from nitrate-free bacon) as a flavorful and often healthier alternative to highly processed oils. Prioritize bacon without added nitrates and preservatives for a cleaner ingredient profile.
  6. Freshly Grated Cheese: For the best melting and flavor, grate your own cheese from a block. Pre-shredded cheeses often contain anti-caking agents that can hinder smooth melting.
  7. Don’t Overfill: While it’s tempting to load up your quesadilla, overfilling can make it difficult to fold, cook evenly, and prevent the cheese from properly melting and binding the tortillas. Stick to a balanced amount of filling.
  8. Even Heat Distribution: Ensure your pan is heated evenly to prevent burning one part of the tortilla while another remains uncooked. Medium-high heat is generally ideal for crisping.

Wholesome and Easy Bacon Egg Cheese Breakfast Quesadilla Recipe:

healthy breakfast quesadillas using whole wheat flour tortillas, bacon with no nitrates, free-range eggs, and freshly grated cheese served with homemade salsa and Crema
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Bacon Egg Cheese Breakfast Quesadilla Recipe

Prep Time: 10 minutes
Cook Time: 5 minutes
Total Time: 15 minutes
Servings: 12 wedges
Author: Alyona Demyanchuk
This is a from-scratch, healthier Bacon Egg Cheese breakfast quesadilla recipe using whole-grain tortillas. We love serving it with sour cream, salsa, or hot sauce. You can fill these “egg cheese sandwiches” with any leftover cheese, veggies, or meat (for extra protein). 

Equipment

  • 10-inch cast-iron skillet
  • Turner
  • 1 mixing bowl (for making scrambled eggs)

Ingredients

Ingredients:

  • 6 slices smoked sliced bacon (No nitrate added)
  • 6 free-range eggs
  • 1/4 cup whole milk
  • 6 whole wheat flour tortillas (8-inch tortillas)
  • 2 1/2 cups shredded Mexican cheese (10 oz block of Monterey Jack or Colby Cheese can be grated)
  • 1/4 tsp salt
  • 1/4 tsp black pepper

Instructions

Directions:

  • browned bacon slices for quesadillas
    Brown the bacon: In a cast-iron skillet over medium heat, fry the bacon slices until crisp.
  • beaten eggs with milk and seasonings for breakfast quesadillas
    Prep the eggs: Meanwhile, whisk the eggs, milk, 1/4 tsp salt, and 1/4 tsp of pepper in a medium mixing bowl.
  • img 18645 8
    Remove bacon onto paper towels and pour the bacon grease into a bowl, reserving 1-2 Tbsp of bacon grease for the eggs.
  • cooked scrambled eggs
    Cook the eggs: Pour the beaten egg mixture into the skillet. Cook until scrambled and cooked thoroughly. Remove the eggs with a slotted spoon and wipe clean the pan.
  • Assembled breakfast quesadillas (whole wheat flour tortillas, cheese, eggs, bacon, cheese, flour tortilla)
    Make the Quesadillas: Arrange three flour tortillas over the countertop and evenly divide cheese, scrambled eggs, bacon pieces, and more cheese for the quesadillas to glue together. Top with the other three tortillas.
  • fried breakfast quesadilla in a skillet
    Cook until crisp: Saute the quesadillas in 2 Tbsp of the reserved bacon grease* over medium-high heat until golden and crisp on each side and the cheese melts.
  • breakfast quesadilla cut into wedges
    Cut into wedges: using a sharp knife or pizza cutter, cut the double-decker quesadillas into quarters. I like to cut it into 4 quarters and serve it with sour cream, Pico De Gallo, or salsa.

Notes

  • You can substitute avocado oil with the bacon grease for a lighter option.
  • When arranging egg quesadillas, the cheese should predominate to ensure good “glue” and gooeyness. Go light on the eggs and meat to prevent overfilling.
  • For sheet pan breakfast quesadillas (oven-baked), arrange four tortillas over a baking sheet. Scatter the cheese, eggs, and bacon, and top with tortillas. Drizzle with oil and bake for 12-15 minutes at 350°F (176°C) until golden and melted.
  • Spicy: Add one seeded and diced jalapeño or sprinkle some red pepper chili flakes for extra heat.
  • Tex-Mex: Sauté bell peppers and onion until tender before adding to the quesadillas for enhanced flavor.
  • Avocados: Top your finished quesadillas with fresh slices of avocado for a creamy, healthy addition.
  • Sausage or Chorizo: Brown your favorite breakfast sausage or chorizo and drain excess grease before adding it to the filling for a different protein option.
  • Beans: For added protein and fiber, drain and rinse a can of your favorite beans (like black beans) and include them in the filling.
  • My Favorite Variation: While my children love the basic egg, bacon, and cheese version, I personally enjoy these with more veggies. Cook 4-6 slices of bacon in a skillet. Remove the bacon, then sauté one diced onion, one diced bell pepper, and a tablespoon of pickled jalapeño slices in the bacon grease until softened. Stir in one cubed avocado. Assemble as instructed; this variation adds so much more depth and flavor!

Nutrition per serving

Serving: 1wedgeCalories: 230kcalCarbohydrates: 12gProtein: 11gFat: 15gSaturated Fat: 7gPolyunsaturated Fat: 1gMonounsaturated Fat: 5gTrans Fat: 1gCholesterol: 110mgSodium: 380mgPotassium: 80mgFiber: 2gSugar: 1gVitamin A: 342IUCalcium: 204mgIron: 1mg