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My recipe for easy homemade jalapeño cheddar bagels is absolutely bursting with peppery, cheesy flavor thanks to fresh jalapeños and cheddar cheese grated right into the dough. For extra heat, the bagels are finished with a jalapeño egg wash, more jalapeño slices, and a generous heap of grated cheddar cheese on top.

Eight jalapeño cheddar bagels are arranged on parchment paper. Sliced and whole jalapeños, along with a small bowl of shredded cheese, are also present. Cheese and jalapeño slices are scattered around the bagels. — If you're looking for a fun weekend baking project, cheddar jalapeño bagels only take a couple hours to make!

As with all my other easy bagel recipes, this jalapeño cheddar bagel recipe uses my standard under 3-hour plain bagel recipe as a base. I've adjusted the ingredients just a bit to accommodate the jalapeños and cheddar cheese in the dough, but the process is otherwise the same.

They bake up so beautifully with a gorgeous crispy cheesy crust and a mild-to-moderate heat with plenty of zesty fresh jalapeño flavor. I am so excited for you to give this bagel recipe a try.

Here's everything you'll need to make these jalapeño cheddar bagels. No fancy ingredients here — this should all be pretty easy to find in most grocery stores.

A top-down view of labeled ingredients for jalapeño cheddar bagels on a tiled surface: a bowl of flour, a bowl of jalapenos, cheddar cheese cubes, water, sugar, yeast, an egg, and a small bowl of salt. — *See recipe card for ingredient quantities.*

I use jalapeños in the dough, and then I also mix them into the egg wash, and I slice some to put on top of the bagels. For the dough, I use 100 grams of grated jalapeños. How many jalapeños you will need depends on how big the peppers are! I lucked out and my local grocery store had some truly monster-sized jalapeños on offer while I was testing this recipe; I needed about 4-5 large jalapeños for a single batch of bagels. If your grocery store has smaller jalapeños, you may need more like 8-10. Err on the side of more jalapeños than you think you'll need.

I tested this bagel recipe with both Extra Sharp and Medium cheddar cheese and found I preferred the less aggressive flavor of the medium cheddar.

Using other types of peppers: You can absolutely experiment with using different types of hot peppers in this bagel dough. Depending on the moisture content of those peppers, you may need to adjust the hydration of the dough to get it to that ideal low hydration, smooth and slightly tacky stage. And depending on the Scoville level of the peppers, you may end up with bagels that are MUCH hotter than these are. So while yes, you can use other hot peppers in these bagels, proceed with caution.

Seven round jalapeño cheddar bagels, some topped with sliced jalapeños, are arranged on parchment paper with cubes of cheddar cheese in a wooden bowl. Slices of jalapeño and shredded cheese are scattered around.

Grated Jalapeño and Cheddar Add A LOT Of Flavor to the Dough

These jalapeño cheddar bagels aren't just plain bagels topped with cheddar and jalapeño slices. Oh no. No no. You deserve better than that from me.

We're going to carry those cheddar and jalapeño flavors throughout the dough. To do that, the first step in this recipe involves finely grating fresh, whole jalapeños.

The heat in jalapeños comes primarily from the seeds and ribs. Using a very fine grater keeps the seeds out. I usually add about a quarter of the seeds to my dough, but you can add more or less depending on how spicy you want your bagels to be.

A gloved hand grates green chili into a measuring cup on a scale, then stirs the green chili mixture with a spatula—essential steps in preparing jalapeño cheddar bagels. Uncut chilies are visible on the counter. Four steps are shown, each labeled 1 to 4. — **TIP:** WEARING GLOVES IS HIGHLY RECOMMENDED FOR THIS STEP. Getting spicy capsaicin oil off your hands is hard, and it can linger for hours, if not days.

Don't be a hero. When there's about an inch of jalapeño left to hold on to, stop grating and move on to the next pepper. Once you've grated the peppers, mix them with the water. This bright green mixture will be the liquid content for the bagel dough.

A hand grates a block of orange cheese into a stand mixer bowl filled with flour, preparing the base for homemade jalapeño cheddar bagels. The bowl is placed on a digital kitchen scale on a white countertop. — Grate the cheese into the dry ingredients.

A metal mixing bowl with flour and a pool of jalapeño water sits on a white tiled surface, ready for the next step in making jalapeño cheddar bagels. The ingredients have not yet been mixed together. — Grate the cheese into the dry ingredients.

Mixing the dough with a dough whisk or with the paddle attachment just until the liquid is absorbed and there are large dry clumps in the bowl makes kneading the dough with the dough hook in the mixer much more efficient.

Normally I jump straight to the dough hook and let it do the mixing, but the pepper bits in the water means it takes a bit longer to absorb.

A metal mixing bowl containing partially mixed dough for jalapeño cheddar bagels, with visible flour and a stand mixer attachment, placed on a white tiled surface. — There is plenty of liquid, it just absorbs more slowly because of the peppers.

Once I've got my large clumps, I switch to the dough hook and finish mixing that way. When the dough forms rough, messy ball and has gathered on the dough hook, I let the dough hook knead away until the dough is elastic and slightly tacky to the touch.

Unlike some of my other bagel doughs, the dough in this homemade bagel recipe may not look particularly smooth. As long as it feels smooth and slightly tacky to the touch, that's okay.

How to Shape a Bagel

Divide the dough into equal portions. Use a kitchen scale to be precise, or trust your gut and just eyeball it.

If you're combining a few pieces together, stack the smaller pieces on top of the bigger pieces. Flatten the dough gently against the countertop with the heel of your hand.

Tuck the edges of the dough up so the dough is smooth against the counter with a seam pinched together on top. Repeat until the dough ball feels fairly tight.

Flip the dough over so the seam side is down against the counter. Cup your hand around the dough and slide it toward you. The dough will take on an oval shape. Rotate it 90 degrees and repeat to turn the oval into a round circle. Repeat as needed.

animated gif: pieces of dough stacked on top of each other with the smaller pieces on top of the bigger ones — step 1: stack dough

animated gif: the edges of the bagel dough being tucked up hiding the smaller pieces in the center — step 1: stack dough

Once the dough has been shaped into balls, let it rest for 10 to 15 minutes covered with a damp paper towel. It needs the time to rest and get used to the new shape.

To make the holes, dust your hands in flour and stick your thumb through the bottom seam of the dough.

Slide your other thumb in next to it and gently squeeze and stretch, rotating the dough through your hands until the bagel hole is at least twice the width of the sides of the bagel, if not bigger.

The dough will naturally shrink back as it rests before boiling. And the hole will also shrink during the boiling and baking steps as the dough expands.

To get a larger hole in your bagels, repeat the stretching process right before boiling to keep the hole from closing up in the oven.

Bagels are Boiled Before Baking

If your bagels aren't boiled, they aren't bagels. Boiling the shaped bagels gelatinizes the starches in the crust. This locks the bagel shape in place and gives the bagels their distinctive shiny, chewy crust.

I boil these cheddar-jalapeño bagels in batches, about 1 minute per side. Then I brush the bagels with the jalapeño egg wash and top them with thin slices of jalapeño and a generous heap of grated cheddar cheese.

A hand grates a block of cheese over unbaked jalapeño cheddar bagels topped with sliced jalapeños on a baking sheet. A bowl with more cheese cubes is in the background. — How much cheese? For these homemade cheese bagels, follow your heart.

If any freshly grated cheese falls onto the sheet pan between the bagels, carefully fish it up with your fingertips and place it directly on top of the jalapeño slices. The cheese helps anchor the peppers in place and protect them from burning in the oven.

A cheddar jalapeño bagel cut in half reveals a creamy filling. Other bagels, cheese cubes, jalapeño slices, and a butter knife are nearby on a white surface, alongside fresh jalapeño cheddar bagels. A stack of plates and a potted plant are in the background.

Practical Tips & Recipe Notes

WEAR GLOVES WHILE GRATING JALAPEÑOS. The capsaicin in the flesh of the peppers is what makes them spicy, and once it settles into the grooves of your fingers, it's really hard to get off. It can stay there for hours, sometimes even days, and is really unpleasant if you forget and rub your eyes. I recommend wearing kitchen gloves (or even just hold the peppers through a plastic bag) while you grate them to keep your hands clean. Just make sure not to accidentally grate any glove into the mix!
If you're particularly sensitive to capsaicin, you may also want to wear gloves while shaping this homemade bagel dough. The flour and water in the dough helps dilute the capsaicin's intensity, but better safe than sorry.

💭 Have More Bagel Questions?

I've rounded up answers to common bagel questions and how-to guides, including:

How to knead bagel dough by hand and what it should feel like
Why bagels are always boiled
Step-by-step guides for bagel shaping and baking techniques

See my bagel-making 101 guide for more!

📖 Recipe

Cheesy, Flavorful Jalapeño Cheddar Bagels

Servings bagels

Author Rebecca Eisenberg

These easy jalapeño cheddar bagels get their bold flavor from fresh jalapeños and cheddar cheese grated right into the dough. For extra heat, they're finished with a jalapeño egg wash, more jalapeño slices, and a generous heap of grated cheddar cheese on top.

Print Recipe Pin Recipe

Prep Time 30

Cook Time 20

Resting & Boiling Time 1 20

Total Time 2 10

Recipe Notes

Eat or freeze jalapeño cheddar bagels within 3 days of baking. Store bagels at room temperature in a brown paper bag or airtight container with a paper towel to absorb moisture. Bagels should not be refrigerated.
Soft jalapeños? Freeze them! If your jalapeños seem to be a bit soft or have thinner walls and you think you'll struggle grating them, freeze them first. You can grate them from frozen, and they'll be much sturdier to hold!
WEAR GLOVES WHILE GRATING JALAPEÑOS. The capsaicin in the flesh of the peppers is what makes them spicy, and once it settles into the grooves of your fingers, it's really hard to get off. It can stay there for hours, sometimes even days, and is really unpleasant if you forget and rub your eyes. I recommend wearing kitchen gloves (or even just hold the peppers through a plastic bag) while you grate them to keep your hands clean. Just make sure not to accidentally grate any glove into the mix!
If you're particularly sensitive to capsaicin, you may also want to wear gloves while shaping this homemade bagel dough. The flour and water in the dough helps dilute the capsaicin's intensity, but better safe than sorry.

Ingredients

Cheddar Jalapeño Bagel Dough

100 grams jalapeños (3-4 large or 4-8 small)
180 grams lukewarm water
500 grams all-purpose flour
50 grams medium sharp cheddar cheese (coarsely grated)
18 grams sugar
10 grams diamond crystal kosher salt
6 grams instant yeast

Cheddar Jalapeño Bagel Topping

1 large egg (for egg wash)
1-2 teaspoons grated jalapeño
1 cup medium sharp cheddar cheese

Instructions

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Grate the jalapeños. Using a fine paddle grater, grate jalapeños into a bowl or liquid measuring up on top of a kitchen scale until you have 100 grams of grated jalapeño. The seeds will collect on top of the grater; for spicy bagels, sweep all or some of the seeds into the bowl, for mild bagels keep the seeds out of the bowl. Set aside any excess grated jalapeños to use in the egg wash later.

Wearing gloves is strongly encouraged for this step! If you don't wear gloves, wash your hands extremely well with soapy water immediately after grating and please DO NOT TOUCH YOUR EYES.

Make jalapeño water. Add the lukewarm water to the jalapeños in the measuring cup and stir well. Set aside.
Combine dry ingredients. In the bowl of a stand mixer whisk together flour, salt, sugar, and yeast. Use an extra coarse grater to grate 50 grams of medium cheddar cheese into the bowl and mix well to distribute the cheese evenly and coat it with flour.
Add the jalapeño water. Pour the jalapeño water into the center of the dry ingredients. (If you're in a humid environment, hold back about ⅛ cup water and add it only if needed.)

If your kitchen is humid, hold back about ⅛ cup of the jalapeño water and add it in gradually only if absolutely necessary.

Mix. Use a spatula to mix the dough together until it's lumpy and starts to clump together, evenly distributing the liquid as best as possible. Then place the bowl in the mixer with the dough hook attached. Mix on low-medium speed until the dough comes together in a messy ball.

Depending on how finely you grate the jalapeños, you may need to add more water or flour to get the dough just right. If the dough hasn't come together after 3 minutes, sprinkle additional ½ teaspoon water onto any dry bits in the bowl and let the mixer run for another 30-45 seconds. Repeat again only if needed. The goal is to get the dough to come together while adding as little water as possible.

Knead. Once the dough has come together on the dough hook, increase the speed to medium and knead for 3-5 minutes until the dough clears the sides of the bowl and is smooth and slightly tacky to the touch.

If the dough suddenly seems too wet or is sticking to the bowl, dust in flour 1 tablespoon at a time. If it still seems dry or like it's tearing instead of kneading smoothly, dip your fingers in water and flick a few water droplets onto the dough as it kneads.

Rise. Shape the dough into a ball and place in a lightly greased bowl. Cover and let rise 1 hour in a warm spot (72-75°F) until just about doubled in size. When you press a finger into the dough the indentation should fill back in just slightly.
Punch down. Punch the dough down in the bowl to knock any large air bubbles out of it. Cover and let rest an additional 10 minutes.
Divide and shape. Use a kitchen scale to divide the dough into 8 equal pieces. On a clean, unfloured counter, shape each one into a ball; Stack any smaller pieces on top of the biggest piece. Gently flatten the dough against the counter, then tuck the edges up into the center, flip the dough over so the seam side is down, and cup your hand around it in a claw shape. Keep your pinkie on the counter and move in tight circular motions to build tension on the top of the dough and smoosh the edges together underneath.
If that doesn't work for you: After flipping the dough over, cup your hand around the dough and, with your pinkie on the counter, pull your hand straight toward your body. The dough will tighten up into an oval shape. Rotate 90° and repeat to pull the oval into a circle shape. Repeat as needed.
Rest. Cover the dough balls with a damp paper towel and let them rest for 10-15 minutes so the seams underneath have time to seal up.
Preheat the oven and water bath. While the bagels rest, preheat the oven to 420°F. Fill a wide, straight-sided skillet with about 3" of water and bring to a low boil. Line a sheet pan with a silicone mat or parchment paper.
Poke the holes. Dust your hands lightly with flour. Poke your thumb through the bottom of each bagel round, pushing any edges or seams into the center. Gently squeeze to stretch (don't tear!) the bagels until the hole in the center is about 2X the width of the bagel sides.
Boil. Working in batches, boil the bagels 1 minute per side. Stretch each bagel again briefly before adding to the pot. Use a wire spider to remove the boiled bagels to the prepared sheet pan.
Top. In a small bowl whisk together 1 egg and 1-2 teaspoons grated jalapeño. Brush each bagel with the egg wash, top with thinly sliced jalapeños, and use a medium sized paddle grater to grate an abundance of cheddar cheese on top of the bagels. Carefully scoop any cheddar that falls onto the parchment paper back on top of the bagels if you can.
Bake. Bake the bagels for 20 minutes at 420°F.
Cool. Let bagels cool on the sheet pan 5 minutes, then remove to a wire rack to finish cooling completely.

Video

Bagels Cheddar Cheese Spicy

Comments

4.82 from 11 votes (1 rating without comment)

Foolproof Jalapeño Cheddar Bagels

Grated Jalapeño and Cheddar Add A LOT Of Flavor to the Dough

How to Shape a Bagel

Bagels are Boiled Before Baking

Practical Tips & Recipe Notes

💭 Have More Bagel Questions?

📖 Recipe

Cheesy, Flavorful Jalapeño Cheddar Bagels

Recipe Notes

Ingredients

Cheddar Jalapeño Bagel Dough

Cheddar Jalapeño Bagel Topping

Instructions

Cook ModePrevent your screen from going dark

Video

Leave a Reply Cancel reply

Grated Jalapeño and Cheddar Add A LOT Of Flavor to the Dough

How to Shape a Bagel

Bagels are Boiled Before Baking

Practical Tips & Recipe Notes

💭 Have More Bagel Questions?

📖 Recipe

Cheesy, Flavorful Jalapeño Cheddar Bagels

Recipe Notes

Ingredients 1x2x3x

Cheddar Jalapeño Bagel Dough

Cheddar Jalapeño Bagel Topping

Instructions Cook ModePrevent your screen from going dark

Video

Comments

Leave a Reply Cancel reply

Ingredients

Instructions

Cook ModePrevent your screen from going dark