Looking for the perfect recipe for jalapeno cheddar bagels? Well, today’s your day my friend: Because these delicious homemade bagels are not only as good as they look, they’re also really easy (and fast!) to make.
I love this cheddar cheese/jalapeño flavour combo, as well as the look of the crispy cheese on top and green flecks of jalapeño throughout. Surprisingly, these bagels are not as spicy as you might think – just accented with the flavour of jalapeño, which is a perfect complement to the cheddar cheese smothering the tops. Also, for some reason (like my Asiago Bagels), I find that cheesy bagels always have the BEST texture, which is so incredibly satisfying!

Serving jalapeño cheddar bagels
Slather one of these up with cream cheese, some good quality butter, or throw some bacon and egg on there to make a sandwich. These bagels are a winner, no matter how you slice ’em! Cheddar jalapeño bagels are the best, in my opinion, toasted before they are served, but after that – A world of delicious serving options awaits you.
How to make homemade bagels, step-by-step
This jalapeño cheddar bagel recipe is super beginner-friendly. (If you want to see what the step-by-step process looks like, you can check out my Asiago Bagels post for a great visual.) I’ll break down the steps for you here, however, in case this gives you a good overview:
- First, make the dough. This simple, stiff bagel dough is made with dry active yeast and a few simple ingredients. Rather than using fresh jalapeños, this recipe uses dried jalapeño, making it easy to have what you need on hand at any time of the year. You can use all purpose flour or bread flour to make this recipe, and make sure to use a large bowl (so that the dough has room to rise).
- Now, the dough will need to proof. Cover with plastic wrap, and then let the dough rise until doubled at room temperature. I find that my bagel dough is usually perfect after about 45 minutes to 1 hour (active dry yeast makes this process happen fairly quickly).
- After the first rise, punch out the excess air from the dough, and shape it into a large dough ball. Divide this into 3 equal sections, and then cut each section into quarters.
- Roll each piece of dough into a long 12″ rope, and then pinch the ends firmly together into a bagel shape with about a golf-ball sized hole in the center of each. Allow the bagels to rest for 10 minutes.
- Poach the bagels in boiling water with honey (my easy alternative to barley malt syrup) for 1 minute on each side (the bagels will double in size during this step).
- Place the bagels on a parchment lined baking sheet and sprinkle generously with sharp cheddar cheese over top of the bagels.
- Bake at a high temperature until golden brown and sizzling. Cool on wire racks.
There you have it! Delicious jalapeño cheddar bagels, fresh from your home kitchen! Scroll down for my printable recipe card, which gives all the details on how to make the dough etc.

Getting the dough just right
Although I am definitely a “Measure by cups” kinda gal, making bread and bagels has changed me a little bit. I like to use a kitchen scale for measuring my flour, just to make sure that I don’t overdo it.
Bagel dough is best when it is quite stiff (it will relax as it rises), but you don’t want to measure compacted cups of flour and end up with something that’s too dry, either. Did you know that measuring flour by cup can give you a range of 100g-170g, depending on how you scoop it? That means that depending on how you scoop it, you may end up doubling a recipe’s flour by accident!
In this recipe, I assume that each 1 cup of flour = 140g. If you don’t have a kitchen scale, try scooping out 1 cup less flour than the recipe suggests, and adding the rest as needed to make a stiff (but still soft and pliable) dough.
If you already messed it up, don’t throw your dough away! As odd as it might sound, add about Tbsp of water at a time and work it back into the dough with the dough hook on your stand mixer. It will look strange at first, but eventually it will work itself into the dough and soften it a little bit. You can add more if needed, but better to add it in slow increments than accidentally make your “too stiff” dough too soft.
Giving the bagels a spicy twist
You can add a little extra heat to these bagels by adding some thinly sliced fresh jalapeños to the top (with the cheese), or even sauté some minced jalapeños in butter before adding them to the dough. Just make sure you cool the jalapeños before you add them to the dough.

Do you need to boil bagels before baking them?
Yes. Otherwise, they would not be bagels! That delicious chewy texture and glossy sheen that bagels have are a direct result of the boiling process. So don’t skip this important step!
Substitutes for barley malt syrup in bagels
If you’ve checked out other bagel recipes in the past, you have probably observed that many of them call for something called barley malt syrup. This gives the dough a distinct traditional bagel flavor, typically found in New York style bagels. It also helps to create the bagel texture.
Making bagel dough without barley malt syrup
For my recipes (since barley malt syrup is not a common ingredient in the average baker’s cupboard), I use a blend of honey and molasses to give my bagels a very similar flavor and texture.
Boiling bagels without barley malt syrup
I like to boil my bagels in a large pot of water with honey, but you can boil bagels a number of different ways to get slightly different results. Here are some good options:
- Salt (a couple of teaspoons added to the water gives the bagel crust a salty flavor)
- Baking soda (about a teaspoon – makes the bagel crust a flavor similar to soft pretzels)
- Molasses (about a tablespoon- gives the bagel crust a rich flavor and slight sheen)
- Brown sugar (a couple of teaspoons – makes the bagels have a sweeter crust)
- Honey (as directed in the recipe below – makes the bagels just slightly honey-kissed and glossy)
- Nothing! Yup, that’s right. Bagels can be boiled with absolutely nothing in the water – they just won’t have that little bit of extra flavour.

Choosing the best cheese
Homemade jalapeño cheddar bagels are best made with a good quality sharp cheddar cheese. My preference is to use orange cheddar (rather than white) just for the look of it. You can use either one with great results, however.
Storage
You can store your homemade bagels in an airtight container or in a sealed plastic bag. (I like to use large, gallon ziploc bags for mine.) Bagels will last at room temperature for a couple of days. They tend to spoil faster in hot/humid weather, and will become stale over time as well.
I like to make a lot of bagels at a time (several dozen) and freeze them for future use. Bagels will keep well in the freezer for a couple of months.
To make this recipe, you will need:
- Ingredients (see recipe card)
- Mixing bowls
- Stand mixer (optional)
- Measuring cups and spoons
- Glass measuring pitcher
- Stirring spoon
- Sharp knife
- Cheese grater
- Large pot
- Round slotted spoon/Cooking skimmer
- 2 Forks
- Kitchen timer
- Baking sheets
- Parchment paper
- Cooling rack
See my Asiago Bagels recipe for step-by-step photos of the bagel making process.


Jalapeño Cheddar Bagels
As opposed to the 12-24 hour period you need to make most bagels, these cheesy bagels can be sizzling out of your oven in just 2 hours. No special ingredients required.
Ingredients
- 1-1/2 cups lukewarm water
- 1/2 Tbsp sugar
- 1 Tbsp dry active yeast
- 2 Tbsp oil olive oil or vegetable oil
- 2 Tbsp liquid honey
- 1-1/2 tsp molasses fancy/table molasses or blackstrap – table molasses is my preference
- 1 tsp salt
- 2 cloves fresh garlic minced
- 2 jalapeño peppers seeded and minced
- 1 egg beaten
- 5 cups all-purpose or bread flour
- 2-3 cups sharp cheddar cheese grated
Poaching Syrup:
- 1/2 cup liquid honey
- 16 cups water 16 cups = 1 gallon
Instructions
-
In a large mixing bowl, combine the lukewarm water with sugar and yeast, and stir to dissolve (there may be small clumps that don’t blend in very well – this is okay). Allow this mixture to rest about 10 minutes, or until slightly risen and bubbly.
-
Sauté the minced garlic and jalapeño peppers in a bit of oil until soft and fragrant; set aside to cool.
-
Add the oil, honey, molasses, salt, beaten egg, and cooled jalapeño/garlic mixture to the yeast/water mixture; stir to combine. Stir in the flour, and knead on a lightly floured work surface until smooth and elastic, about 3-5 minutes. Place the dough back into the bowl, cover with plastic, and allow to rise 1 hour or until doubled.
Note: To test if the dough is risen enough, stick your finger into the dough – if an indentation remains without shrinking back where your finger was, it is ready to use.
-
While the dough is rising, combine the water and honey for the poaching syrup in a large pot and bring to a boil. Reduce heat to a simmer, just to keep it hot, until ready to use.
-
When the dough has risen enough, punch it down to remove any air bubbles. Turn it out onto a clean work surface. Divide the dough into 12 evenly divided portions (each should weigh about 100 grams).
-
Roll each portion of dough into a long rope, about 12 inches long. Bring the ends together with about a 1-inch overlap, pinching the ends together firmly to seal. Roll over the pinched portion of dough a couple of times, with your hand in the hole of the bagel, to make the seam a little smoother and more uniform. Set the finished bagel onto a parchment lined baking sheet, and repeat with the other bagels until all 12 have been shaped. The holes in the centre of the just-shaped bagels should be large enough to fit a golf ball inside snugly.
Note: If the dough is sticky, you can use a little flour on the work surface to prevent sticking. Also, I like to make my bagel holes a little smaller, so I usually roll them with 3 fingers in the hole instead of my whole hand.
-
Bring the poaching syrup back to a boil, preheat the oven to 425 degrees Fahrenheit, and allow the bagels to rest 10-20 minutes, or until about 1-1/2 times their original size. They won’t look very much larger – just slightly more puffy.
-
Drop 3-5 bagels into the boiling poaching syrup (depending on the size of your pot – you want them to have room to expand without overlapping each other), and allow them to poach 1 minute on each side, but not longer. If anything, take the bagels out slightly before they reach the 1 minute mark per side. Lift the bagels out of the water using a slotted spoon or fork, allowing them to drip slightly before setting them onto a parchment-lined baking sheet. The bagels should double in size during this step.
-
Allow the bagels to cool slightly, and then re-attach the ends of any bagels that broke open during the poaching process. Sprinkle the bagels generously with grated cheddar cheese. (The dough should be a sticky, spongy texture at this step.)
-
Bake at 425 degrees Fahrenheit for 12-15 minutes or until golden brown. Cool on wire racks.
Recipe Notes
1 cup flour = 140 grams in this recipe.
IMPORTANT: When dealing with jalapeño peppers, it’s important to wear plastic disposable gloves and to refrain from touching your face, especially around your eyes. I once burned myself with jalapeños, working with unprotected hands – so please, be careful! Wash your hands well when you’re finished chopping them, and discard the used gloves.



If you like this recipe, you may also like:
As always, feel free to leave questions in the comments – and, if you make them, I’d love to hear how they turn out! You can tag me in your gorgeous bagel photos on Instagram @naomicakesofficial – I love to see what you’re making!
Thanks for stopping in,
Naomi
This post contains affiliate links.