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.

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.
Too busy to make this right away? Pin it for later! Pin this post to your favorite board on Pinterest and it will be there when you’re ready!
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!

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.

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.

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.

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.

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.

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.

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.

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.

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.

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!

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.

Gluten-Free Jalapeno Cheddar Bagels (Air Fryer Recipe)
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.