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Gluten-Free Jalapeno Cheddar Bagels (Air Fryer Recipe)

Enjoy the spicy kick of homemade gluten-free Jalapeño Cheddar Bagels with this easy recipe! Perfectly golden and packed with cheesy goodness, these bagels are a treat for breakfast or anytime.

A bagel topped with melted cheese and three slices of jalapeño, sitting on parchment paper with small holes. The bagel is golden brown and appears freshly baked.

There’s something so satisfying about making your own bagel recipe from scratch. No need to rely on a grocery store for those overpriced, dry bagels when you can whip up greek yogurt bagels right at home!

Plus, these are protein bagels, thanks to the plain Greek yogurt, so they pack a little extra nutrition into each bite.

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Why You’ll Love This Recipe

These homemade bagels are not only gluten-free but also bursting with flavor. The combination of sharp cheddar and spicy jalapeño gives them a unique twist that’s perfect for breakfast or as a savory snack. And they’re easy to customize with your favorite toppings!

A cheesy pastry with a bite taken out, topped with jalapeño slices, rests on parchment paper. Shredded cheese and jalapeño slices are scattered around it on a wooden surface.

This is the next level of homemade baking—forget the long fermentation process required for traditional bagels. No active dry yeast and no waiting for the dough rise!

These bagels are ready in about 30 minutes, making them a great way to start your morning or meal prep for later use.

Top-down view of five bowls on a wooden surface. They contain gluten-free flour, cheddar cheese, Greek yogurt, jalapeño, and baking powder. Each ingredient is labeled.

Ingredients

  • Greek yogurt – the key to keeping these bagels soft and chewy.
  • Gluten-free flour blend – a necessary swap for those avoiding all purpose flour or looking for gluten free bagels.
  • Cheddar cheese, shredded – because a cup of the cheese makes everything better!
  • Jalapeño pepper, diced – fresh or pickled diced jalapeños add the perfect spicy kick.
  • Baking powder – helps the bagel dough rise and keeps them light.
A glass bowl with dough containing green and orange bits sits on a wooden table. Nearby are sliced jalapeños and shredded orange cheese in a small round dish on a lace cloth.

Instructions

1. In a large mixing bowl, combine the gluten-free flour blend and baking powder.

2. Stir in the plain Greek yogurt, diced jalapeños, and half of the shredded cheddar until a dough ball forms.

3. Divide the dough into three equal pieces.

Three unbaked, circular bagels with bits of vegetables are placed on a parchment-lined baking sheet.

4. Roll each piece of dough into a ball, then press a hole into the center of each ball to create the classic bagel shape.

5. Line your air fryer basket with non-stick spray and parchment paper.

A bagel topped with shredded cheese and three jalapeño slices is placed on a piece of parchment paper inside an air fryer basket. The bagel appears uncooked, with a white doughy texture.

6. Place the bagels inside (one at a time), press the remaining cheddar onto the top of each bagel, and add extra fresh jalapeños if desired.

7. Air fry at 300°F for 15-20 minutes until golden brown.

A bagel topped with melted cheese and jalapeño slices sits on parchment paper inside an air fryer basket. The parchment is slightly burnt at the edges. A small dish of green garnish is partially visible in the corner.

For multiple batches, bake on a parchment-lined baking tray in the oven at 350°F for 20-25 minutes.

The Secret to Perfect Shaped Bagels

The key to making shaped bagels that look as good as they taste is handling the dough correctly. If the dough sticks, use wet hands or dust a lightly floured surface before shaping.

A bagel topped with melted cheddar cheese and sliced jalapeños, resting on parchment paper.

If you want a shinier crust, brush the tops with an egg wash before baking. This will also help any toppings—like poppy seeds or more cheese—stick better.

If you’re a stand mixer fan, you can also use a dough hook to mix everything together, making this process even easier. Just be sure to stop mixing as soon as the dough comes together; overworking it can make the bagels tough.

A bagel topped with melted cheese and sliced jalapeños sits on a piece of parchment paper. In the background, there is a bowl with shredded cheese and scattered jalapeño slices on a wooden surface.

Tips & Tricks

  • Wet or dust hands with flour for easy dough shaping.
  • Smooth out bagel tops for prettier results.
  • Substitute Greek yogurt with cottage cheese for extra protein.
  • Get creative with toppings like cinnamon sugar or olive oil and kosher salt for a sweet or savory touch.
A hand holds a freshly cooked bagel topped with melted cheese and slices of jalapeño. The bagel is being lifted from the basket of an air fryer. A small dish with green herbs is partially visible in the background.

Frequently Asked Questions

Can I make these dairy-free?
Sure! Swap plain Greek yogurt for thick dairy-free options like coconut or almond-based yogurt.

Can I use regular flour instead of gluten-free flour?
Absolutely! Substitute gluten-free flour blend with all purpose flour or bread flour if gluten isn’t a concern.

How do I store leftovers?
Store in an airtight container at room temperature for a day or refrigerate for up to 3 days. Reheat in the air fryer for 4-5 minutes to freshen up. These are best served warm as they harden over time.

Can I freeze the bagels?
Yes! Once cooled, freeze in a single layer on a baking tray, then transfer to a freezer bag. Reheat directly from frozen in the air fryer at 300°F for a couple of minutes – they are best enjoyed fresh or heated.

A hand holds two pieces of a cheese-stuffed, golden-brown biscuit or bread with jalapeño slices on top. The bread appears soft and fluffy, with melted cheese visible. A bowl with shredded cheese and jalapeño slices is in the background.

These gluten free jalapeno cheddar bagels are a great way to enjoy the flavor of traditional bagels without the gluten! Whether you’re spreading them with cream cheese, using them for sandwiches or just enjoying them plain, this recipe is one you’ll want to make again and again.

Be sure to check out these cottage cheese bagels or high protein bagels too!

A cheddar jalapeno Greek yogurt bagel on parchment paper. The bagel is topped with melted cheddar cheese and jalapeno slices. Text at the bottom reads cheddar jalapeno Greek yogurt bagels homemadeheather.com.

If you love these jalapeno cheddar bagels, please give them a five star rating by clicking the stars below! Help me share them on Facebook or Pinterest so that others can try them too.

A bagel topped with melted cheese and three slices of jalapeño, sitting on parchment paper with small holes. The bagel is golden brown and appears freshly baked.

Gluten-Free Jalapeno Cheddar Bagels (Air Fryer Recipe)

Savor the spicy kick of homemade Gluten-Free Jalapeño Cheddar Bagels with this easy recipe! Perfectly golden and packed with cheesy goodness, these bagels are a treat for breakfast or anytime.
No ratings yet
Prep Time: 10 minutes
Cook Time: 15 minutes
Servings: 3 servings
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Ingredients

  • 1 cup Greek yogurt
  • 1 cup Gluten-free flour blend
  • ½ cup cheddar cheese shredded
  • 1 Tbsp Jalapeño pepper diced
  • 1 tsp Baking powder

Instructions

  • In a large mixing bowl, combine the gluten-free flour blend and baking powder.
  • Stir in the plain Greek yogurt, diced jalapeños, and half of the shredded cheddar until a dough ball forms.
  • Divide the dough into three equal pieces.
  • Roll each piece of dough into a ball, then press a hole into the center of each ball to create the classic bagel shape.
  • Line your air fryer basket with non-stick spray and parchment paper.
  • Place the bagels inside (one at a time), press the remaining cheddar onto the top of each bagel, and add extra fresh jalapeños if desired.
  • Air fry at 300°F for 15-20 minutes until golden brown.

Notes

  • Wet or dust hands with flour for easy dough shaping.
  • Smooth out bagel tops for prettier results.
  • Substitute Greek yogurt with cottage cheese for extra protein.
  • Get creative with toppings like cinnamon sugar or olive oil and kosher salt for a sweet or savory touch.
  • These are best eaten fresh or reheated as they harden over time.
  • Store in an airtight container for a day or two or in the freezer for weeks.

Nutrition

Serving: 1serving | Calories: 253kcal | Carbohydrates: 33g | Protein: 15g | Fat: 8g | Saturated Fat: 4g | Polyunsaturated Fat: 0.5g | Monounsaturated Fat: 2g | Trans Fat: 0.003g | Cholesterol: 22mg | Sodium: 289mg | Potassium: 121mg | Fiber: 4g | Sugar: 4g | Vitamin A: 245IU | Vitamin C: 6mg | Calcium: 313mg | Iron: 2mg
about heather

Hello, I’m Heather!

I'm an active mom of twin boys who is always looking for opportunities to inspire creativity through fun crafts, do-it-yourself projects and delicious recipes. This blog has been an integral part of supporting my little family and I am so grateful to have you become a part of our journey! Let's create together... Read more...

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