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Made from scratch and ready to eat in 90 min, these Cheddar Jalapeño Bagels are completely beginner friendly, loaded with cheese and jalapeños right in the dough. It will be the best Jalapeño Cheese Bagel you’ll ever have.

a jalapeno cheddar bagle on a counter top next to some sliced jalapeños.

Get ready to fall in love with this Cheddar Jalapeño Bagel Recipe

I have become absolutely OBSESSED with making bagels, so much so I have dubbed the year 2024 as the year of the bagel, that way you never need to buy dry, hard, flavorless bagels at the grocery store again.

Today’s feature, CHEDDAR JALAPEÑO BAGELS! I decided to use some diced canned jalapeños right inside of the dough to push that jalapeño flavor throughout the entire bagel, not just on top. Plus, no dicing for you AND you don’t have to keep fresh jalapeños on hand if the craving strikes.

Sharp cheddar cheese also goes inside of the dough as well as on top, because, we can never have too much cheese. Get your kneading arms ready, and let’s learn how to make these bad boys!

(pst, if you’re new here, I have been publishing one new bagel recipe a week, so go browse the recipes I already have and comment any suggestions you have!)

cheddar jalapeno bagels on a cookie cooling rack.

Jalapeno Bagel Ingredients

Exact amounts for each ingredient can be found in the printable recipe card below. Check out the list below to find tips, tricks and possible substitutes.

  • Water– Just tap water will work fine! This water needs to be warm in order to activate the yeast. I always check the temp of my water with my instant read thermometer. We are shooting for 105° F- 113° F.
  • Dry Active Yeast– You can use the packets or a larger jar that you’ll measure out of. You can find this down the baking aisle.
  • Brown Sugar– Generally bagel shops use barley malt in their bagels, brown sugar is a good substitute for the barley malt. This helps feed the yeast and sweetens the dough ever so slightly.
  • Bread Flour– yes. Bread Flour. It has extra protein in the flour that will keep your bagel fresh for longer and lend to the chewy texture bagels are known for. I am usually a ‘all-purpose is fine- kind of person, but the bread flour makes a huge difference here.
  • Salt
  • Sharp Cheddar Cheese– I always shred my own cheese for these bagels- I love Tillamook’s Sharp Cheddar Cheese, but you can use whatever brand is your favorite.
  • Canned Diced Jalapeños– I like to use the canned kind inside of the dough because they are guaranteed to be soft and not crunchy inside of the bread and it saves so much time by not needing to dice them yourself.
  • Fresh Jalapeños– while not completely necessary since we will get the jalapeño flavor from the diced ones in the dough, it is really fun to but sliced rounds of jalapeños on top of the bagels along with the shredded cheese while baking.

Bagel Making Tools

jalapeno cheddar bagels on the pan before baking.

How to Make Jalapeño Cheddar Bagels

  1. First, activate the yeast by combining the yeast with the warm water and brown sugar. Allow the mixture to sit for 5-10 minutes. It should become very bubbly and foamy, this means that the yeast is activated and your bagels will rise. If nothing happens, then your yeast hasn’t activated and it is dead. Throw the mixture out and try again. It could have died from too hot or cold water, or your yeast may be expired.
  2. Combine the remaining ingredients in either a large bowl or the bowl of a stand mixer while the yeast is activating. The remaining ingredients are the bread flour, salt, some shredded cheddar cheese and diced jalapeños.
  3. Once the yeast is activated, pour the liquid into the dry ingredients. Either stir and knead by hand or with the stand mixer. For more detailed instructions on each, read the printable recipe card below.

How to Shape Bagels

  1. To shape the bagels, you first need to divide your dough into 8 equal sized pieces. The easiest way to do this is by cutting the entire batch of dough in half. Then cut each of those halves in half again, giving you 4 equal sized pieces. Last, cut each piece in half one last time to give you 8 equal sized pieces.
  2. Working with one portion of dough at a time, push and pull the dough on the counter to create tension while rolling into a ball.
  3. Flatten the ball slightly and then press your thumb into the center of the dough. Slowly stretch and pull the dough while moving the dough around your thumb until you achieve the bagel shape.
  4. Repeat with the remaining dough portions and then place on a covered silicone lined cookie sheet to rise for 20 minutes.

How to Boil Bagels

  1. While your bagels are rising, fill a large pot with about 4 inches of water and bring to a rolling boil.
  2. Drop two risen bagels into the boiling water at a time.
  3. Allow the bagels to boil for 1 minute and then use a spider strainer to flip the bagels over before boiling for an additional minute.
  4. Using the spider strainer, remove the bagels from the water and place back on the silicone lined cookie sheet.
  5. Repeat with the remaining bagels.
  6. While the next pair of bagels are being boiled, place 3 sliced jalapeño coins onto the top of the bagel and sprinkle generously with shredded cheddar cheese.
  7. Once all of the bagels have been boiled and are topped with some jalapeño slices and shredded cheese, they are ready to bake.

How to Bake Jalapeño Bagels

  1. Bake your bagels in a 425° F oven for 15-19 minutes, or until golden brown.
  2. Allow the bagels to cool on the pan for 5-10 minutes before slicing and enjoying.
jalapeno cheddar bagels on a striped dish towel.

Jalapeño Cheddar Bagel Tips

  • Remember you can always add more flour to your dough, but it’s hard to take it out. Start with the suggested 4 1/2 cups of flour and if your dough is still sticking to your hands, then add more flour 1 tbsp at a time. The dough should be soft and tacky, but shouldn’t stick to your hands.
  • Feel free to use more diced jalapeños in your dough!
  • If your bagels deflate when you touch them to put into the boiling water, you most likely let them rise for too long. Either that or there wasn’t enough flour added to the dough.

How do you eat Jalapeño Bagels?

I love to eat mine with cream cheese- reminds me of a jalapeño popper! These also make killer sandwiches, add some sliced deli meat, lettuce, veggies and you’ve got yourself a delicious lunch.

pin image for cheddar jalapeno bagels

Jalapeño Cheese Bagel FAQ

Are jalapeño cheddar bagels spicy?

No, I don’t find them spicy! You’ll just get the flavor of the jalapeno pepper coming through but none of the heat.

Can you put cream cheese on a hot bagel?

Yes, and in my professional opinion, you should. 🙂

Does Cheddar Jalapeño bread need to be refrigerated?

Nope! You are fine to store these bagels at room temp for up to 3 days or in the freeze for up to 3 months.

More Bagel Recipes

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Jalapeno Cheese Bagel

Made from scratch and ready to eat in 90 min, these Cheddar Jalapeño Bagels are completely beginner friendly, loaded with cheese and jalapeños right in the dough. It will be the best Jalapeño Cheese Bagel you'll ever have.
Prep Time: 45 minutes
Cook Time: 15 minutes
Resting Time: 30 minutes
Servings: 8 bagels


  • 2 cups warm water, (105°F-113°F)
  • 1 1/2 tbsp dry active yeast
  • 1 tbsp brown sugar, packed
  • 4 1/2 cups bread flour, plus 2-3 tbsp, as needed
  • 2 tsp salt
  • 2 cups shredded cheddar cheese, divided
  • 2-4 tbsp canned diced jalapeños
  • 2 jalapeños, sliced into rounds


  • In a small bowl, add the warm water, dry active yeast and brown sugar. Stir to combine and set aside.
  • In a large bowl or in the bowl of a stand mixer, add the 4 1/2 cups of bread flour, salt, 1/2 cup of shedded cheese and the canned diced jalapeños. Stir to combine.
  • Your yeast mixture should be bubbly and foamy. Add the yeast mixture to they dry ingredients.
  • If using a stand mixer, use the dough hook and knead for 10 minutes, you will most likely need to add the extra 3 tbsp of flour to keep the dough workable but soft.
  • If mixing by hand, start by stirring the dry ingredients into the yeast mixture until a shaggy dough forms. At this point, pour the contents onto a clean surface and knead by hand for 10 minutes.
  • Add the extra 2-3 tbsp of bread flour as needed to keep the dough soft but workable.
  • Knead by Pushing the dough, turning and folding it in half. Repeating this for 10 minutes.
  • Once the dough has fished kneading, Allow the dough to rest for 5 minutes.
  • Use a sharp knife or bench scraper to cut the dough into 8 equal sized pieces. (Cut the dough in half, then each half in half again and then once more)
  • Take each portion of dough and knead into a tight ball. Once in a ball, press your thumb into the center of the ball and gently squeeze and pull the dough while rotating it around your thumb to create the bagel shape. Place onto a parchment or silicone lined 3/4 cookie sheet (this is just a larger cookie sheet).
  • Repeat with the remaining dough.
  • Cover the cookie sheet with plastic wrap and allow the bagels to rise for 20-30 minutes.
  • In a large pot, boil about 4 inches of water and preheat the oven to 425° F.
  • Once the water is at a rolling boil, carefully drop the risen bagels into the boiling water one by one. You may have to do this in a few batches.
  • Boil the bagels for 1 minute, flip over to the other side and boil for an additional minute.
  • Using a large slotted spoon or spider strainer to remove the bagels and return to the lined cookie sheet.
  • Repeat with the remaining bagels. While the next batch of bagels are boiling, top the boiled ones with 3 sliced jalapeño rounds and shredded cheddar cheese.
  • Once all of the bagels have boiled and are topped with shredded cheese, bake in the 425° F oven for 15-17 minutes or until golden brown.
  • Allow the bagels to cool for 10 minutes before cutting and enjoying.
  • Store in a zip top bag at room temperature for up to 3 days.


Calories: 378kcal | Carbohydrates: 54g | Protein: 15g | Fat: 11g | Saturated Fat: 6g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Cholesterol: 28mg | Sodium: 834mg | Potassium: 109mg | Fiber: 2g | Sugar: 2g | Vitamin A: 348IU | Vitamin C: 0.4mg | Calcium: 215mg | Iron: 1mg
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About Karli Bitner

This blog is a little glimpse into my kitchen, family & life. I hope you’ll giggle the days away with me and enjoy the craziness that goes on at my house. If you are Cookie obsessed like I am, check out my Sister Site, Cookies for Days.

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