Start by adding 3 1/4 cups of bread flour, 2 1/4 tsp instant yeast, 1 tsp salt, 1 cup warm water and 2 tsp of malt syrup or honey into the bowl of a stand mixer or a large bowl.
Knead either by hand or with a dough hook on a medium-low speed for 1 minute, then add in 1/2 cup diced jalapeños and 2/3 cup finely grated cheddar cheese.
Continue mixing on a medium speed or kneading by hand until the dough is elastic but firm (about 10 minutes by hand or 5 minutes with a dough hook).
You may need to add in a bit of extra water or flour if the consistency of the dough is off, but do so slowly (1 Tbsp at a time).
Spray the inside of separate large bowl with non-stick spray to prevent the dough from sticking and place the dough ball into this bowl to rest.
Cover with a kitchen towel place in a warm place for about 15 minutes. This gives the dough a chance to rest, which relaxes the gluten and will make the dough easier to roll out and shape.
Turn the dough out onto a floured surface. Knead the dough for a few minutes until it's nice and smooth again, then cut it into 9 equal pieces. You can use a scale if you really want to be sure each bagel ends being the same size.
Roll each piece of dough into a strip long enough to wrap around your fingers (about 7-8 inches long). Connect the two ends of the loop, and roll the ends together on your counter until they stick together. If your ends aren't sticking together, dab a tiny bit of water onto them to help them stay put.
Place the rolled bagels on a baking tray lined with parchment paper to rest. Let them rest while you bring your water to a boil.
Bring 5-6 cups of water to a boil in a large pot. When the water is gently boiling, add 1 Tbsp of baking soda.
At this point, preheat your oven to 425 F.
Place 2 bagels into the pot at a time, and let them cook for 45 seconds on each side. I don't recommend boiling more than 2 at a time or else they'll be overcrowded and difficult to flip.
As the bagels are boiled, remove them and place them on paper towels (to absorb excess moisture). Repeat with the remaining bagels.
When all the bagels are boiled, move them from the paper towels to a parchment lined baking sheet. They will feel a bit slimy, but that's how they're supposed to be!
While the bagels are still moist, top with finely shredded cheese and 1 sliced jalapeno.
Bake at 425ºF for 18-22 minutes, rotating the pan halfway through. The cheese on top of the bagels bagels should be a relatively dark golden brown and their crust should be quite firm.
Let them cool on the tray until they cool down enough to handle (about 15 minutes), then slice and enjoy.
Leftover bagels can be stored in an airtight container at room temperature for up to 3 days or in the refrigerator for up to a week.