
Mini Protein Jalapeño Bagels with Cheddar are my new favorite breakfast! Smear with cream cheese, or use them to make sandwiches! These are leavened with baking powder and Greek yogurt so they pack a nice protein punch!

Don’t get me wrong, I love a traditional bagel as much as the next person.
But these jalapeño cheddar bagels are made with Greek yogurt and add way more protein to your diet than a typical bagel, which I also love.
And the absolute best part about these homemade bagels is that you don’t need to be a baker to make them.
Unlike traditional bagels, which require yeast fermentation and gluten development, these are made without yeast and don’t require any boiling. This means, yes, they won’t have that extremely chewy texture that traditional bagel dough has. Nor will it have molasses or sugar, warm water, and all the other ingredients you typically add to feed the yeast and develop a dough.
But what they will have is a slightly chewy texture similar to biscuits. It’ll also be ready in less than half the time of a traditional bagel and not require a stand mixer.

Plus, the fact that it has way more protein doesn’t require active dry yeast, and has the extra step of having to boil bagels in boiling water. Bonus: if they’re flavored with minced and jalapeño slices and speckled with sharp cheddar cheese, you can totally sign me right up.
This is an easy and straightforward jalapeño cheddar bagel recipe that doesn’t require a dough hook, instant yeast, bread flour, malt syrup, a pot of water, or a slotted spoon!
If you can add all-purpose flour, salt, baking powder, and some Greek yogurt to a bowl, you can make protein bagels at home in a flash!

Ingredients for Protein-Rich Cheddar Jalapeño Bagels
- All-purpose flour: I have good news for you! Both all-purpose and bread flour will work for this recipe. The higher the protein in the flour, the crisper these bagels will be. Most high-protein bagel recipes call for self-rising or self-raising flour. This is something I rarely have in the pantry. So, I went ahead and made the recipe with regular flour. If you have self-rising flour at home and want to use it, see the notes under the recipe card on what ingredients you’ll need to swap out!
- Baking Powder: this is the leavening agent in our recipe. We’ll add the baking powder and kosher salt to our dough and let it hang out for 5-10 minutes. This allows the baking powder to really be absorbed by the other ingredients and leaves us with one protein-packed bagel!
- Kosher Salt: pretty self-explanatory here! Use sea salt or kosher salt.
- Garlic Powder: gives the bagels just a hint of garlicky goodness. Think of it as a supporting actor, you won’t know it’s there front and center.
- Jalapeños: you’ll need at least two jalapeños. The first one you’ll mince up and add to flavor the dough before kneading. The second jalapeño gets sliced up and gets specked on top of the bagels so that they give the top a beautiful edible appearance!
- Sharp Cheddar Cheese: I like to get a block of cheddar cheese and grate it myself. Store-bought shredded cheese contains fillers such as potato starches (and corn), which sometimes prevent the cheese from sticking to the bagel. For this reason, I prefer to shred the cheese on a coarse grater and knead it into the dough.
- Greek Yogurt: I like using full-fat Greek yogurt for this recipe. My favorite is Chobani Whole Milk or Fage 5%. 2% or even 0% will work. I do suggest using a higher fat percentage if possible, though. I find it gives the bagels a better taste. And yes, vegan Greek yogurt should work well in place of traditional Greek yogurt!
- An Egg: This is to egg wash the bagels with before we sprinkle them with more cheddar cheese and speckle with a few jalapeño slices.

Making Jalapeno Cheddar Bagels
- Start the prep work. You’ll want to preheat the oven and line a baking sheet with parchment paper. Then, set this aside for now.
- Combine the dry ingredients. In a bowl, combine the flour, baking powder, kosher salt, and garlic powder until mixed. Then, stir in the jalapenos and cheddar. Sometimes, it’s easier to do this with a fork so that the peppers and cheese are nicely coated in the flour mixture and evenly distributed throughout the dough.
- Mix the dough. Add the Greek yogurt to the dough and then using your hands turn and fold the dough ingredients until they come together. Take your time here and really work the dough without adding water or more flour. If the dough doesn’t come together, then add a teaspoon of room-temperature water or flour and work it until the dough comes together.
- Shape the bagels. Divide the dough into equal pieces. I usually make 11 pieces because I want them to be mini! Then, roll the dough out into a 5-inch rope. Roll the ends together to join. Place the bagels on the baking sheet.
- Brush and speckle them for perfection. Brush the bagels with the beaten egg, and if desired, sprinkle with the jalaeño slices and cheddar cheese.
- Bake and serve. Bake the bagels on the prepared baking sheet in the oven until they’re golden brown on top. Remove the bagels to a wire rack and let them finish cooling.

FAQs about this recipe
If by taste you mean the flavor, then yes! But if you mean the texture, then no. They will definitely have a less chewy texture than a typical bagel because we aren’t developing the gluten the same way.
Keep the bagels at room temperature for 1-2 days and consume or keep them in the fridge if you anticipate them to be around longer. For long-term storage, pop them into a freezer-safe bag and freeze them for up to 3 months.
If your toaster has a bagel setting, I’d use that! Slice the bagels down the center and then toast for 2-3 minutes.
This really depends on your definition of ‘healthy.’ If you’re looking for a bagel recipe that’s higher in protein and contains only a handful of ingredients, this definitely meets the definition!
You can use some butter, smashed avocado, cream cheese, or a scrambled egg with some bacon. It would also make a mean tunacado! I also love my breakfast sandwiches for a more protein-packed meal – just swap the English muffins for these bagels!
You can follow my original protein bagel recipe to make sesame bagels or everything bagels!
Other breakfast recipes to try
- Homemade Jalapeño Cheddar Bread
- Savory Zucchini Muffins with Cheddar Cheese
- How to Make Egg Bites (in the Oven!)
- Tex Mex Migas Breakfast Tacos
- Easy No Knead Bread

Protein Jalapeño Bagels with Cheddar Cheese
Mini Protein Jalapeño Bagels with Cheddar are my new favorite breakfast! Smear with cream cheese, or use them to make sandwiches! These are leavened with baking powder and Greek yogurt so they pack a nice protein punch!

Ingredients
- 3 cups all purpose flour
- 5¼ teaspoons baking powder
- 1 teaspoon kosher salt
- ⅛ teaspoon garlic powder
- ¼ cup minced jalapeños
- ½ cup shredded sharp cheddar cheese, plus more
- 2 cups greek yogurt
- 1 large egg, lightly beaten
- 20-24 jalapeño slices (thin, for topping)
Instructions
- PREP: Position a rack in the center of the oven and preheat the oven to 375ºF. Line a baking sheet with parchment paper; set aside.
- DRY: In a bowl, whisk the flour, baking powder, salt, and garlic powder. Then mix in the minced jalapeños and the cheddar cheese and combine.
- MIX: Add the greek yogurt and mix together until a dough forms. You might want to use your hands to make this easier! If the dough is too dry, add a teaspoon of water until the dough comes together. Alternately, if it’s too wet add a teaspoon of flour and more as needed. It just depends on the humidity in the room.
- DIVIDE: Turn the dough out onto a clean surface. Divide it out into 8 equal pieces. You can weigh the dough balls if you want to be extra precise.
- SHAPE: the dough into a smooth ball. Then place your thumb through the center of the ball. Gently pull the dough (counter clockwise for a righty) around your thumb to help stretch and make the bagel larger. Place the bagels on the prepared baking sheet and let sit for 5-10 minutes if possible. This allows the bagels to puff up a bit more.
- BRUSH AND SPECKLE: brush bagels with the beaten egg. Sprinkle with a bit more cheddar cheese, if desired, and speckle with a couple slices of jalapeños.
- BAKE: Place the pan in the oven and bake the bagels for 12-15 minutes or golden brown on top. Remove the bagels to a wire rack and let them rest for 10 minutes or until cooled so you can slice them. Toast if desired and spread with cream cheese. Store leftover bagels in an airtight container for up to 4 days.
Notes
- Variations: you can season these with everything bagel seasoning, sesame seeds and so much more. Check out my other high protein bagel recipe here.
Nutrition Information:
Yield:
10Serving Size:
1Amount Per Serving: Calories: 229Total Fat: 5gSaturated Fat: 3gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 32mgSodium: 480mgCarbohydrates: 34gFiber: 2gSugar: 3gProtein: 12g
The nutrition information is provided as a courtesy and is just an estimate. To get the most accurate information, please input the ingredients you've used into a nutrition calculator.