Jalapeño Cheddar Protein Bagels: Delicious Recipe

Isabella

Modified:February 13, 2026

Published:February 13, 2026

by Isabella Mansouri

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Intro: My Go-To Protein Bagel

As a passionate home baker constantly seeking ways to elevate my morning routine, I embarked on a mission to create the ultimate high-protein breakfast that didn’t compromise on flavor or texture. And let me tell you, these Jalapeño Cheddar Protein Bagels are the triumphant result! Imagine biting into a wonderfully soft yet chewy bagel, with pockets of sharp, melty cheddar and a zesty kick of fresh jalapeño in every savory mouthful. It’s the kind of breakfast that not only satisfies your cravings but also keeps you feeling full and energized. I’ve been experimenting with protein-packed breakfasts for ages, and when I stumbled upon the magic of a two-ingredient dough, fortified with protein, it opened up a world of possibilities. Adding the bold flavors of spicy jalapeño and sharp cheddar cheese transformed it from a good idea into a truly irresistible, unforgettable treat. This recipe is a game-changer for anyone looking for a wholesome yet utterly delicious start to their day. For more delicious and easy-to-follow recipes like this one, you can See more easy recipes on my blog.

Why This Recipe Works

  • Perfect Chewy Texture: The combination of self-rising flour and Greek yogurt creates a surprisingly tender yet chewy bagel, mimicking traditional bagels without the fuss of yeast proofing.
  • Balanced Flavor Profile: Fresh jalapeños offer a vibrant, adjustable heat that perfectly complements the rich, savory notes of sharp cheddar cheese, making every bite exciting.
  • High Protein, Happy You: This recipe incorporates unflavored protein powder, boosting the nutritional value and ensuring you stay satiated longer, making these bagels an ideal and smart breakfast choice.
  • Golden, Appetizing Crust: An egg wash brushed before baking ensures a beautiful, golden-brown crust with a delightful sheen, trapping in moisture and enhancing the overall appeal.

Ingredients and Substitutions

Here is what you need and why:

Self-Rising Flour: This is the secret ingredient for foolproof protein bagels! Self-rising flour already contains baking powder and salt, simplifying the recipe and ensuring a great rise without needing yeast. If you don’t have self-rising flour, you can easily make your own by combining 1 cup of all-purpose flour with 1 ½ teaspoons of baking powder and ¼ teaspoon of salt.

Plain Greek Yogurt: Essential for both moisture and that classic tangy bagel flavor. It reacts with the self-rising flour to create the perfect dough consistency. It is crucial to use plain, unsweetened Greek yogurt – flavored or traditional thin yogurts will alter the texture and taste significantly. Full-fat or low-fat Greek yogurt works equally well.

Unflavored Protein Powder: This is where the ‘protein’ in our Jalapeño Cheddar Protein Bagels comes from! I highly recommend an unflavored whey or casein protein powder for the best texture and taste integration. Flavored protein powders, especially vanilla or chocolate, will clash with the savory profile of these bagels. Ensure it’s a powder you enjoy the taste of on its own, as some unflavored varieties can have a subtle aftertaste.

Shredded Sharp Cheddar Cheese: For that irresistible cheesy goodness! Sharp cheddar delivers a robust flavor that stands up beautifully to the jalapeño. While pre-shredded cheese is convenient, shredding your own from a block often melts better and has a richer taste. You can experiment with other cheeses like Monterey Jack or a Colby-Jack blend if you prefer.

Fresh Jalapeños: The star of the show for that fantastic spicy kick! Make sure to seed and finely dice your jalapeños for even distribution and adjustable heat. If you like more heat, you can leave some seeds in, but be warned, a little goes a long way! For a milder flavor, you can briefly soak the diced jalapeños in cold water after seeding.

Egg Wash: A simple egg wash (one egg whisked with a splash of water or milk) serves two important purposes: it gives your bagels that beautiful golden-brown, glossy crust, and it helps whatever topping you choose adhere perfectly.

Everything Bagel Seasoning (Optional): A fantastic addition for extra crunch, texture, and a burst of savory flavor. It’s a classic bagel topping for a reason! If you don’t have it, a sprinkle of sesame seeds, poppy seeds, or even a little extra coarse salt would also be delicious.

How to Make Your Best Jalapeño Cheddar Protein Bagels

Follow these step-by-step instructions to bake delicious Jalapeño Cheddar Protein Bagels:

1. Combine Dry Ingredients

In a large mixing bowl, whisk together the self-rising flour and unflavored protein powder until thoroughly combined. This ensures the protein is evenly distributed before the wet ingredients are added.

2. Add Yogurt and Form Shaggy Dough

Gradually add the plain Greek yogurt to the dry mixture. Use a sturdy spoon or a rubber spatula to mix until a shaggy, somewhat crumbly dough forms. It might look dry at first, but keep mixing; the moisture from the yogurt will eventually bring it together.

3. Fold in Cheese and Jalapeño

Turn the shaggy dough out onto a lightly floured surface. Sprinkle the shredded cheddar cheese and finely diced jalapeño over the dough. Gently fold and press the ingredients into the dough until they are mostly incorporated. We’re not looking for perfect distribution just yet, as the next step will help.

4. Knead Briefly Until Smooth

Knead the dough gently for about 1-2 minutes. The goal is to bring the dough together, ensure the cheese and jalapeño are evenly distributed, and achieve a relatively smooth ball. Avoid over-kneading, as this can make your bagels tough. The dough should feel soft and slightly tacky, but not sticky.

5. Divide and Shape into Bagels

Divide the dough into 6 equal pieces. Roll each piece into a log, about 6-8 inches long. Bring the ends of the log together to form a circle and pinch them firmly to seal, creating the classic bagel shape. Alternatively, you can roll each piece into a ball and then use your thumb to poke a hole in the center, gently stretching it to form the bagel hole. Place the shaped bagels on a baking sheet lined with parchment paper.

6. Prepare Egg Wash and Toppings

In a small bowl, whisk one egg with a tablespoon of water (or milk) to create your egg wash. Brush the tops and sides of each shaped bagel generously with the egg wash. If desired, sprinkle with Everything Bagel Seasoning (or sesame seeds, poppy seeds, etc.).

7. Bake Until Golden Brown

Preheat your oven to 375°F (190°C). Bake the bagels for 20-25 minutes, or until they are beautifully golden brown and sound hollow when tapped on the bottom. The cheese should be melted and slightly bubbly. Let them cool slightly on a wire rack before serving to allow the internal structure to set. For further reading on baking perfect bagels, I highly recommend checking out resources from trusted sites like King Arthur Baking.

Expert Tips for Success

  • Don’t Over-Knead the Dough: Gentle kneading for 1-2 minutes is all you need. Over-working the dough can develop too much gluten, leading to tough, dense bagels rather than soft and chewy ones.
  • Finely Dice Jalapeños: Ensure your fresh jalapeños are finely diced. This prevents large chunks that can create holes in the dough or overwhelm a single bite. Even distribution is key for consistent flavor.
  • Adjust Spice Level: For less heat, remove all seeds and the white membrane from the jalapeños (this is where most of the capsaicin resides). For more heat, you can leave a few seeds in, but proceed with caution!
  • Bake Immediately: Once shaped, bake your Jalapeño Cheddar Protein Bagels without delay. This ensures the leavening agents in the self-rising flour are most active, giving you the best rise and texture.
  • Use Parchment Paper: Lining your baking sheet with parchment paper is a simple step that makes a huge difference. It prevents sticking, makes cleanup a breeze, and helps the bottoms of the bagels cook evenly.
  • Quality Ingredients Matter: Using good quality self-rising flour, fresh full-fat Greek yogurt, and sharp cheddar cheese will significantly impact the flavor and texture of your homemade bagels.

What to Serve With Your Jalapeño Cheddar Protein Bagels

These savory Jalapeño Cheddar Protein Bagels are incredibly versatile! Here are some of my favorite ways to enjoy them:

  • Classic Cream Cheese: A smear of plain cream cheese is always a winner. For an extra kick, try a chive & onion cream cheese or even a lightly spiced jalapeño cream cheese.
  • Avocado Slices: Creamy avocado pairs beautifully with the spicy jalapeño and sharp cheddar. A sprinkle of Everything Bagel Seasoning on top of the avocado elevates it further.
  • Breakfast Sandwich: Turn your bagel into a hearty breakfast sandwich! Add a fried or scrambled egg, a slice of crispy bacon or turkey bacon, and perhaps an extra slice of cheddar for a truly satisfying meal.
  • Smoked Salmon: For a sophisticated brunch, top your bagel with a generous portion of smoked salmon, a dollop of cream cheese, and a sprinkle of fresh dill or capers. The flavors are simply divine together.
  • Compound Butter: Whipped butter infused with herbs like chives or a tiny pinch of chili flakes would also be a fantastic accompaniment.

Storing and Reheating

To keep your Jalapeño Cheddar Protein Bagels fresh and delicious:

  • Room Temperature: Store cooled bagels in an airtight container or a large zip-top bag at room temperature for up to 3 days. To maintain freshness, you can also wrap individual bagels in plastic wrap before placing them in the container.
  • Freezing for Longer Storage: These bagels freeze beautifully! Once completely cooled, wrap individual bagels tightly in plastic wrap, then place them in a freezer-safe bag or container. They will keep well in the freezer for up to 3 months. Freezing them individually allows you to grab just one or two as needed.
  • Reheating: For the best texture, reheat thawed or fresh bagels in a toaster or toaster oven until warmed through and lightly crispy. If reheating from frozen, you can often pop them directly into the toaster on a defrost setting, or thaw them overnight in the refrigerator first. You can also warm them in a preheated oven at 350°F (175°C) for about 5-7 minutes.

Frequently Asked Questions

Can I use almond flour?
Unfortunately, almond flour behaves very differently from self-rising wheat flour due to its lack of gluten and different absorption properties. This recipe relies on the gluten structure in wheat flour combined with the Greek yogurt for its chewy texture. Substituting with almond flour would likely result in a very dense, crumbly bagel that doesn’t resemble a traditional bagel texture.
How do I make them gluten-free?
To make these Jalapeño Cheddar Protein Bagels gluten-free, you would need to use a gluten-free self-rising flour blend specially formulated for baking, or create your own by using a gluten-free all-purpose flour blend (one that contains xanthan gum) and adding baking powder and salt as per the self-rising flour ratio (1 cup GF flour, 1.5 tsp baking powder, 1/4 tsp salt). The texture might be slightly different, but many gluten-free alternatives can work. Ensure your protein powder is also gluten-free.
What other cheese can I use?
While sharp cheddar is highly recommended for its flavor, you can definitely experiment with other cheeses! Monterey Jack, Colby-Jack, pepper jack (for an extra kick!), or even a blend of mozzarella and cheddar would work well. Avoid extremely soft or watery cheeses, as they might affect the dough consistency.
Why are my bagels dense?
Several factors can lead to dense bagels. The most common culprit is over-kneading the dough; this develops too much gluten, making the bagels tough and dense. Another reason could be using too much flour during kneading, making the dough dry. Ensure you’re using fresh self-rising flour and plain Greek yogurt, as older or flavored ingredients can impact the rise. Also, make sure your oven is preheated to the correct temperature.
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Jalapeño Cheddar Protein Bagels


  • Total Time: 40 minutes
  • Yield: 6 bagels 1x

Description

Bake delicious, high-protein bagels packed with spicy jalapeño and sharp cheddar cheese. This easy recipe uses simple ingredients for a satisfying breakfast.


Ingredients

Scale
  • 1 ½ cups (180g) Self-Rising Flour (plus extra for dusting)
  • ½ cup (60g) Unflavored Whey or Casein Protein Powder
  • 1 cup (240g) Plain Greek Yogurt (full-fat or low-fat)
  • ¾ cup (90g) Shredded Sharp Cheddar Cheese
  • 12 Fresh Jalapeños, seeded and finely diced (adjust to taste)
  • 1 large Egg, for egg wash
  • 1 tbsp Water or Milk, for egg wash
  • 2 tsp Everything Bagel Seasoning (optional)

Instructions

  • In a large bowl, whisk together self-rising flour and protein powder.
  • Add Greek yogurt and mix until a shaggy dough forms.
  • Turn dough onto a lightly floured surface. Fold in shredded cheddar and diced jalapeños.
  • Knead gently for 1-2 minutes until dough is smooth and ingredients are incorporated.
  • Divide dough into 6 equal pieces. Roll each into a log, form a circle, and pinch ends to seal.
  • Place shaped bagels on a parchment-lined baking sheet.
  • Whisk egg with water/milk for egg wash. Brush bagels, then sprinkle with seasoning if desired.
  • Bake at 375°F (190°C) for 20-25 minutes, until golden brown. Cool on a wire rack before serving.
  • Prep Time: 15 mins
  • Cook Time: 25 mins

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