These easy homemade jalapeño cheddar bagels are absolutely bursting with peppery, cheesy flavor thanks to 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.
If you're looking for a fun weekend baking project, cheddar jalapeño bagels only take a couple hours to make and can be ready in time for brunch!
Thank you so much to Microplane for sponsoring this post. All opinions are my own. And thank YOU so much for supporting the businesses who support The Practical Kitchen! Use code TPK10 for 10% off at Microplane.com!
About Jalapeño Cheddar Bagels
In this post I'm going to walk you through how to make these jalapeño cheddar bagels with plenty of visual cues and tips along the way.
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, though you could also follow this process using my recipe for chewy homemade egg bagels 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 these bagels a try.
(Oh, and if you're looking for something to do with any leftover cheddar and jalapeños, you're going to love my super easy no-knead cheddar jalapeño bread.)
🌶 Ingredient Notes & Substitutes
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.
I've even noted possible ingredient substitutes where relevant. See recipe card for quantities.
- Jalapeños - You'll need jalapeños in the dough, to mix into the egg wash, and to slice and put on top of the bagels. For the dough, you'll need 100 grams of grated jalapeños. How many jalapeños you need will depend on how big your 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 only has smaller jalapeños, you may need more like 8-10. Err on the side of more jalapeños than you think you'll need. If you have any left you can always use them to make cheddar jalapeño no-knead bread or freeze them for later.
- Cheddar Cheese - I tested this recipe with both Extra Sharp and Medium cheddar cheese and I preferred the less aggressive flavor of the medium cheddar. You can absolutely use whatever your favorite cheddar cheese is.
- All-Purpose Flour - I use King Arthur Baking Company's All-Purpose flour which has a slightly higher protein count than most all purpose flours (it's closer to a bread flour). If you can't find King Arthur's All-Purpose flour, you may get better results with another brand's bread flour.
- Salt - I use Diamond Crystal Kosher Salt in all of my recipes which half as salty as other brands. If you're measuring salt by weight, you can use any brand of salt here. But if you're measuring by volume (e.g. teaspoons) and using a different brand of salt, even a different brand of kosher salt, cut the amount of salt in half.
- Sugar - Regular granulated sugar. Nothing fancy.
- Yeast - I use Instant Yeast (sometimes called "rapid rise" yeast) in all of my baking. If you only have active dry yeast, you'll want to use 9 grams instead of 6 grams. Your dough also may also take a little bit longer to rise.
- Water - You want the water to be lukewarm or warm, but not hot. The cooler the water, the slower your dough will rise. But if the water is too hot (115F or above) it can kill the yeast.
- Egg - For the egg wash. It's infused with grated jalapeños to give the bagels a nice spicy coating! It also helps the cheese and the jalapeño slices stick to the bagels.
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 paddle grater or Microplane 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.
TIP: WEARING GLOVES IS HIGHLY RECOMMENDED FOR THIS STEP. Getting spicy capsaicin off your hands is really hard, and it can linger for hours if not days. I will repeat this tip a few times throughout this post. It's that important.
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 lukewarm water. This bright green mixture will be the liquid content for the bagel dough. Set it aside.
In the bowl of your stand mixer, mix together the flour, salt, sugar, and yeast. Try to keep the yeast and salt from sitting right on top of each other — the salt can kill the yeast if they're in contact for too long.
Grate in the cheddar cheese using a large, coarse grater. You want short strands of cheddar cheese here, not long ones.
Mix the cheese into the dry ingredients so all the strands get coated in flour. This prevents them from clumping up inside the dough.
Then make a well in the center of the dry ingredients and pour the bright green jalapeño water into the middle.
Next you're going to use a spatula or your hands (only if wearing gloves!!) to mix everything together.
Normally I jump straight to the dough hook and let it do the mixing, but the pepper bits in the water means it'll take a bit longer to absorb.
There is plenty of liquid, it just absorbs more slowly because of the peppers.
Mixing the dough by hand first, just until the liquid is somewhat evenly incorporated, will make mixing and kneading much more efficient.
Now switch to the dough hook. Mix on low-medium speed just until the dough comes together in a rough, messy ball. If it hasn't come together after 3 minutes, flick some water droplets on to the dough and mix a little longer.
When the dough has gathered on the dough hook, it's time to knead. Increase the speed to medium and let the dough hook knead away for 3-5 minutes until the dough is smooth, slightly tacky, and elastic.
Unlike some of my other bagel doughs, this dough may not look particularly smooth at this stage. As long as it feels smooth and slightly tacky to the touch, that's okay.
Shape it into a ball, place it in a lightly greased bowl, cover it, and let it rise for about an hour. It may not completely double in size, but it will come close. When you press a finger into it, the indentation should spring back slowly.
Before shaping the bagels, gently deflate the dough and let it rest for 10 minutes.
🥯 How to Shape a Bagel - With Gifs!
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.
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.
🌡️ Boiling & Baking Bagels
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.
Boil the bagels in batches, about 1 minute per side. You can go up to 2 minutes per side for a chewier bagel.
Then brush the bagels with an egg whisked together with about a teaspoon of grated jalapeño. Top the bagels with thinly sliced jalapeño, and top with a generous heap of grated cheddar cheese.
How much cheese? 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 will help anchor the peppers in place and protect them from burning in the oven.
🔪 Equipment Notes
You don't need a lot of super fancy tools to make jalapeño cheddar bagels — you might even have some of these in your kitchen already! Here's what I used:
Microplane Select Series Starter Kitchen Set - This set comes with three durable, high quality paddle shaped graters of varying coarseness levels and a microplane. To make these bagels I used all three of the paddle graters.
- The smallest paddle grater ("fine") is perfect for grating the jalapeños - the seeds can't get through the tiny holes. You can use the long skinny Microplane for this step, but the wide flat surface of the paddle grater gives you a little more room to move around.
- The medium sized ("coarse") grater slices the cheddar cheese for topping the bagels into thin ribbons without being too delicate or too heavy that they slide off in the oven.
- The largest ("extra coarse") grater is ideal for grating the cheddar cheese into the dry ingredients in the bagel dough.
Kitchen Scale - As with all baking recipes, using a kitchen scale is worth it for getting the best, most consistent results with this recipe. The ratio of jalapeños to water and ratio of liquid to dry ingredients can dramatically change how your jalapeño cheddar bagels turn out. Those ratios are calculated by weight. I really do encourage you to use a kitchen scale (this is the kitchen scale I use and love). They're very affordable (about $15-20) and will make you a much better baker.
Wire Spider - Wire spiders are wide, wiry scoops that make it easy to flip and remove things in boiling water or oil without splashing everywhere. The wide, shallow shape and closely aligned wires provide plenty of support to your delicate boiled bagels, while the gaps between the wires prevent excess water from getting caught up in the scoop and splashing everywhere.
Disposable Kitchen Gloves - I've said it once, I've said it twice, I'll say it again: USE GLOVES WHEN GRATING JALAPEÑOS. If you don't have disposable kitchen gloves you can use a plastic bag. You just really won't be happy if you skip the gloves all together and then can't get that spicy capsaicin off your fingertips.
🧀 What to Serve With Jalapeño Cheddar Bagels
What do you put on a jalapeño cheddar bagel? There's a lot of flavor already happening in the bagel itself! Here's how I like to eat them:
- Toasted with plain cream cheese or with jalapeño cream cheese for extra heat
- Toasted with homemade butter
- Toasted with cream cheese and bacon
- Toasted with cream cheese and sun dried tomatoes
- As BLTs with ripe summer tomatoes, crispy lettuce, and extra crispy bacon
- With a fried egg and sausage as a breakfast sandwich
- With mashed avocado, salted tomatoes, and quick pickled red onions
How do you like eating jalapeño cheddar bagels? Let me know in the comments!
⏲️ Storage Tips
Jalapeño cheddar bagels should be stored at room temperature in an airtight container or paper bag with a paper towel to absorb moisture.
Due to the cheese and peppers on top, these jalapeño cheddar bagels tend to spoil quickly — plan to eat them within a few days.
If you're not planning to eat them all within a day or two, slice them almost all the way through and freeze. Bagels should not be refrigerated.
👩🏻🍳 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 handling the dough. The flour and water in the dough helps dilute the capsaicin's intensity, but better safe than sorry.
- If you live somewhere humid, hold back about ⅛ cup of the water while mixing and add the rest gradually only if the dough seems very dry. Bagel dough is low hydration which means you want to resist adding water to the dough unless absolutely necessary.
- 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 seems wet and sticky, dust in flour 1 tablespoon at a time while mixing. If the dough seems very dry and looks like it's tearing as it kneads, dip your fingers in water and flick just a few water droplets onto the dry parts of the dough.
- 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!
💭 Recipe FAQ
Absolutely! I only recommend doing this if you're pretty confident handling doughs. Depending on the moisture content of those peppers and the Scoville level, you may need to adjust the hydration of the dough to get it to that ideal low hydration, smooth and slightly tacky stage. You may also 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.
You can, but I don't recommend it. Pre-shredded cheese is usually coated in cellulose or starches, which helps keep it from clumping. There's nothing harmful about it, it's totally safe to eat. But it can make the cheese interact differently with the other dry ingredients and liquids in this dough than if you grated it by hand.
You can make the dough and shape the bagels the night before you plan to boil and bake them. If you're going this route, don't stretch the bagel holes too big when you shape them. Leave them, uncovered, on a sheet pan in the fridge. In the morning, give them another stretch right before boiling. You could also leave the boiled bagels, covered, in the fridge overnight before baking in the morning.
It really depends on how many of the jalapeño seeds you mix into the dough and how diligent you are about removing the seeds from the jalapeño slices on top of the bagels. If you keep most of the seeds out these are very very very very very mild. I promise. If you're looking for spicy, leave all those seeds in, baby!
💭 Top Tip
Be patient with this cheddar jalapeño bagel dough. There are a few resting periods throughout the recipe — this gives the yeast and gluten in the dough time to relax and get used to the new shapes you're asking it to take on.
The dough will move slower in colder environments and faster in warmer ones. So if your kitchen is very cold, the dough may need a bit more time to rest, rise, and relax before you move on to the next step.
Move the dough somewhere warm — a laundry room, an off oven with the light on, on top of the oven while it preheats, etc. — if your kitchen runs cold. This will help speed up the rising time.
Jalapeño Cheddar Bagels
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 (4 teaspoons)
- 10 grams diamond crystal kosher salt (1 tablespoon)
- 6 grams instant yeast (2 teaspoons)
Cheddar Jalapeño Bagel Topping
- 1 large egg (for egg wash)
- 1-2 teaspoons grated jalapeño
- 1 cup medium sharp cheddar cheese
- 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.)
- 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. 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. The bagels will shrink slightly when they boil and bake, so if you prefer a bigger hole, stretch them again right before you boil them.
- Boil. Working in batches, boil the bagels 1 minute per side. 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.
- If your kitchen is humid, hold back about ⅛ cup of the jalapeño water and add it in gradually only if absolutely necessary.
- If you add too much water and the dough feels sticky, or sticks to the sides of the mixing bowl, dust in more flour 1 tablespoon at a time until it pulls clear from the sides of the bowl.
- 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.
- I use King Arthur Baking Company's All-Purpose flour which has a slightly higher protein count than most all purpose flours (it's closer to a bread flour). If you can't find King Arthur's All-Purpose flour, you may get better results with another brand's bread flour.