These easy Greek Yogurt Jalapeno Cheddar Bagels are a cheesy, spicy breakfast packed with 18 grams of protein. No yeast, no boiling, just 7 simple ingredients and big flavor!

You should also try my Greek yogurt blueberry bagels!

Jalapeno cheddar greek yogurt bagels on a board.

Why You’ll Love Jalapeno Cheddar Bagels

Olena Osipov in her kitchen.

You guys all loved my high protein Greek yogurt bagels, so I wanted to create some tasty variations. Jalapeno cheddar bagels were at the very top of my list! Golden outside, soft and chewy inside, packed with amazing flavor and extra protein from Greek yogurt.

It took me 3 rounds of testing to get the consistency just right. Adding cheese made the jalapeno bagels deflate, so I had to increase the flour to help them puff up.

My biggest tip is to measure your flour by weight (I included it!), and due to various factors, go by how the dough feels – it should be pretty thick. That way when the cheese melts there’s enough flour to absorb it.

Ingredients for Jalapeno Cheddar Bagels

There’s no yeast or protein powder in these jalapeno protein bagels. Just a handful of kitchen staples!

Greek yogurt, flour, salt, baking powder, egg, jalapenos, cheddar cheese.
  • All-purpose flour: 9 ounces gives the dough the perfect consistency. I used all-purpose flour for the best soft, chewy texture and rise without yeast. You can swap in whole wheat or gluten-free flour, see variations below.
  • Greek yogurt: I used 2% Oikos, but any fat level works as long as it’s Greek yogurt. Don’t use regular yogurt because it’s too watery. Dairy-free works too, as long as it’s thick like Greek yogurt.
  • Baking powder and salt: The little things that help your bagels rise, taste great, and have the perfect texture.
  • Jalapeños: I diced 1 jalapeno and left the seeds in, then added more slices on top and I would say it was medium heat. You can de-seed the jalapeno before dicing if you want your bagels milder.
  • Cheddar cheese: Freshly grated cheese melts better and gives the best cheesy flavor, but pre-shredded works in a pinch. You can try pepper jack for extra spice or mozzarella for a milder taste.
  • Egg: Used for brushing the bagels to give them a shiny, golden crust.

Self-Rising Flour

You can use self-rising flour instead of flour, baking powder, and salt. Just weigh out the same amount of flour and skip the baking powder and salt since they’re already mixed in.

How to Make Jalapeno Cheddar Protein Bagels

I made sure this bagel recipe is great for all baking levels with easy prep, no boiling, and ready in 1 hour. Full recipe card below.

Step by step process how to make dough for jalapeno cheddar greek yogurt bagels.

Set your oven to 375 F and line large baking sheet with parchment paper.

  • Mix the dry ingredients: Grab a big bowl and whisk together the flour, baking powder, and salt.
  • Add the flavor: Toss in the diced jalapenos and cheese, and whisk to combine.
  • Form the dough: Stir in the yogurt with a spatula, then switch to mixing with your hands until you have a ball of dough. Knead it about 20 times, it should feel firm but not dry or sticky. Cover with a clean towel and let it rest for 10 minutes.
Step by step process how to make jalapeno cheddar greek yogurt bagels.
  • Shape the dough: Lightly flour your counter and place the dough on it. Divide into 4 pieces, roll each into a rope, and pinch the ends to form a bagel shape with a fairly big hole. Then set them on your lined baking sheet.
  • Add toppings: Whisk the egg in a small bowl and brush it over the tops of the bagels. Add sliced jalapenos and a sprinkle of cheese.
  • Bake and rest: Bake for 25-28 minutes until they’re golden and puffy. Once out, let them rest for 15 minutes (trust me, this step matters!). Then slice, top, and enjoy however you like. I made a fried egg sandwich with mine, amazing!

Air Fryer Tip

Once shaped, place the jalapeno bagels in the air fryer basket and cook at 280 F for 15-20 minutes, depending on your air fryer.

Tips for Best Results

Here are some kitchen-tested tips from me to you for making the best jalapeno cheese bagels for your breakfast or snack.

  • Scoop and level the flour: Spoon the flour into the cup and then level it off with a knife. That’s a proper way to measure the flour. Don’t dip into flour.
  • Weigh the flour: Using a kitchen scale is the best way to get the right amount. I had to add a bit more flour to get the dough just right, so weighing helps you avoid guesswork.
  • Make sure dough is thick: It should be thick and feel firm. That way, it holds up when the cheese melts.
  • Ovens vary: Some run hotter or cooler so it’s best to check on your cheese bagels around the 20 minute mark.
  • Let bagels rest: After baking and before slicing. Resting helps finish the cooking process and sets the texture, don’t skip it!
Sliced jalapeno cheddar greek yogurt bagel showing texture.

Variations

  • Gluten-free flour: I usually use Bob’s Red Mill gluten free baking flour. Use it 1:1 ratio like regular flour, but make your bagel logs shorter and the holes smaller since the dough won’t stretch or rise as much.
  • Whole wheat flour: I haven’t tested it yet, but you should be able to use about 7 ounces instead. Whole wheat tends to rise more, so I’d roll the logs a bit longer and make the holes larger so they don’t close up as they bake.
  • No egg wash: You can skip it if needed, but jalapeno cheddar bagels won’t turn out as golden and shiny. Brushing with a little water or melted butter works as a good backup.
  • Adjusting the heat: For a milder kick, remove the seeds before dicing. If you like more spice, keep the seeds in and add extra slices on top.
  • Mini bagels: Divide the dough into 6–8 pieces instead of 4 and shape as usual. Keep an eye on the bake time, they’ll likely need a few minutes less.
  • No jalapeno: Simply omit the jalapeno and everything else stays the same. You’ll still get a soft, cheesy, protein-packed bagel!

How to Store and Reheat

Store: Place your Greek yogurt bagels in an airtight container and keep them in a cool, dark spot. They’re good for 3-4 days.

Freeze: Stash some for later in a Ziploc bag, in the freezer for up to 3 months.

Reheat: Let them thaw on the counter, warm them up in the microwave, or toast them.

More High Protein Recipes to Try

Jalapeno cheese bagel sandwich with an egg.
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Jalapeno Cheddar Bagels (High Protein)

Greek Yogurt Jalapeno Cheddar Bagels are a cheesy, spicy breakfast with 18 grams of protein. No yeast, no boiling, just 7 simple ingredients and big flavor!
Prep: 10 minutes
Cook: 25 minutes
Resting Time: 25 minutes
Total: 1 hour
Servings: 4 bagels

Ingredients 

  • 1 3/4 cups all-purpose flour, (9 ounces), more for dusting
  • 2 teaspoons baking powder
  • 3/4 teaspoon salt
  • 2 medium jalapenos, one diced, one sliced
  • 1/3 cup cheddar cheese, shredded, more for garnish
  • 1 cup Greek yogurt, I used 2%
  • 1 egg, beaten

Instructions 

  • Preheat oven to 375 degrees F and line large baking sheet with parchment paper. Set aside.
  • In a large bowl, add flour, baking powder and salt; whisk well. Add diced jalapeno and cheddar cheese, whisk until incorporated.
  • Add Greek yogurt and stir with spatula to combine, then proceed to mix with your hands until a ball of dough forms. Knead it about 20 times. Dough should be not sticky but not dry and quite firm. Cover with a towel and let rest for 10 minutes.
  • Transfer dough on a counter sprinkled with flour, form into a round and cut into 4 even pieces. Roll each into a long rope and then pinch the ends into a bagel shape, making a large hole as bagels puff up. Place on a previously prepared baking sheet.
  • In a small bowl, whisk the egg. Brush bagels with an egg wash, top with sliced jalapenos and cheddar cheese.
  • Bake for 25-28 minutes or until golden brown and puffy. Remove from the oven and let rest for 15 minutes (do not skip!). Slice, spread and enjoy with your favorite toppings.
🎉 Last step! If you made this recipe, please leave a review and let us know what you think!

Notes

  • Store: Keep in an airtight container in a cool dark place for 3-4 days.
  • Freeze: Freeze in a resealable Ziploc bag for 3 months. Thaw on a counter for a few hours or pop into microwave or toaster.
  • Air fryer: You can also air fry bagels at 280 F for 15-20 minutes, depends on air fryer.

Nutrition

Serving: 1 bagel, Calories: 344kcal, Carbohydrates: 52g, Protein: 18g, Fat: 6g, Saturated Fat: 2g, Trans Fat: 0.01g, Cholesterol: 53mg, Sodium: 743mg, Fiber: 2g, Sugar: 2g

Nutrition information is automatically calculated, so should only be used as an approximation.

Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!
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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 14 years making it my mission to help you cook quick and easy meals for your family!

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