Chewy and flavorful sourdough bagels using only freshly milled flour! This bagel recipe is loaded with savory bacon, cheddar cheese, and jalapeno pieces. It isn’t too spicy and it makes the most delish and wholesome bagel for ham sandwiches! Even kids rave about how good these are! I share how easy it is to make these Jalapeno cheddar bagels with my step-by-step tutorial! 

Jalapeno cheddar sourdough bagels made with freshly milled flour

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Whole Wheat Sourdough Bagels are a favorite, toasted and smeared with probiotic cream cheese, but the Jalapeno Cheddar Bagel takes it to the next level! 

Sure, you can make Jalapeno cheddar sourdough bread by adding cheddar cheese and jalapeno slices to the dough, but every individual bagel is super chewy and crisp, which is not the case with a regular artisan slice. 

The bacon adds so much flavor and texture to these sourdough bagels. We have quite a harvest of hot peppers from our garden, so it is only appropriate to make cheddar jalapeno bagels. 

jalapeno cheddar sourdough bagels

You could use pickled jalapeno peppers, too, but don’t skimp on the fresh bacon. The bacon grease lends superior crispness and flavor to these bagels! 

We like to have sandwiches at the farmhouse on rotation, so making bagels instead of whole-wheat hamburger buns is a lovely change. 

I crave these bagels for my ham sandwiches, and my whole family enjoys them just as much! Stuff them with fresh veggies or any deli meat for a quick lunch, or serve them as individual breads with a bowl of soup. To make it extra special, serve it with some cream cheese for a “jalapeno poppers” bagel. 

jalapeno cheddar bagels

A Glimpse Of My Baking Schedule:

If preparing and baking bagels seems like a big task, I’m here to tell you it’s very easy!

As busy as my days can get with homeschooling, blogging, and all the mundane tasks, I can make these bagels in less than 30 minutes with about 5 minutes of hands-on work. The mixer does the rest, and then it ferments and keeps in the fridge until the next day, in time for lunch. 

It’s not as time-consuming as you think. Besides, it’s worth every minute of my time because the kids are thrilled, and nothing compares to the aroma of sweet and spicy jalapeno peppers, smoky bacon, and cheddar cheese all in one bite!  

You need to try these flavorful sourdough bagels, and the fact that they are made with 100% freshly milled wheat makes me joyous!  

How do I do it? I’ll feed my sourdough starter in the early morning, make my sourdough bagel dough at noon (it only takes me a few seconds to mill my grain with this grain mill), let the dough sit out for about 4 hours, and then hide it in the fridge. All of this takes very little hands-on work and my family can enjoy warm and fresh bagels like the bakery!  

Ingredients For Jalapeno Cheddar Bagels: 

  • Sourdough Starter: Make sure your starter is active and bubbly. This will give a good rise and make the bagels fluffy and chewy. 
  • Dough- This sourdough bagel dough is healthy because it uses 100% whole grains. I weigh my hard white wheat grain on a scale and then run it through a grain mill. As I do that, I prepare the other ingredients, including frying the bacon (which takes minutes). 
  • Jalapenos—I use fresh jalapenos from my garden. You could use pickled jalapenos, but they will be more acidic. Using fresh peppers gives you the option of choosing milder hot peppers if you wish. 
  • Cheddar Cheese—I use a box grater with large holes to shred a block of sharp cheddar cheese. The cheese goes into the dough and the tops for a crispy crust and appearance. 
  • Thick-cut Bacon: I fry two slices of chopped bacon in a skillet until they turn brown and crisp. Transfer the bacon to a bowl and let it cool while you get the other things going. You don’t want to add it to piping hot dough, as that can kill the starter. 

Can I Use Different Grains? 

Yes, any hard wheat variety is ideal for making bagels. You need the gluten in hard wheat to achieve chewy bagels, so mix and match any hard variety, like hard red. A great start is hard white wheat, which is mild in flavor and similar to the flavor of all-purpose flour. If you want to add a low-gluten grain such as soft white wheat, add in a little amount however, you may need to add extra vital wheat gluten to make a stretchy dough. 

sliced jalapeno cheddar bagel

Handy Equipment: 

I use an electric grain mill to make whole wheat flour in seconds. I do not recommend measuring the flour without a scale; the grams will give you the most accurate results. Working with freshly milled flour takes longer to bring together, so winging it based on the look can be a little misleading. Use a heavy-duty stand mixer to get the kneading done unless you want to have an arm workout:) 

How To Make Jalapeno Cheddar Bagels Using Freshly Milled Flour: 

  1. Mix The Sourdough Bagel Dough, adding the water, starter, diced jalapenos, chopped bacon pieces (including all the bacon grease), cheese, honey, and flour. Knead for 15-20 minutes, then add the salt and knead for 5 more minutes. The longer you knead the freshly milled flour dough, the more you work out the gluten, so it’s okay to knead it for a total of 25 minutes. 
  2. Fermenting: Place the dough in a glass bowl with a lid and let it ferment for 4 hours. I sometimes perform stretch and folds, but you can completely skip those and still have amazing results. Because it kneads long, the gluten structure is already worked out, so stretch and folds are optional. The dough will look sticky, but it should be smooth and stretchy.
  3. Refrigerate the bagel dough. You could bake these bagels the same day. However, I tend to make multiple breads on my sourdough baking day, so breaking up some of my baking allows me to finish it the next day. You can refrigerate for 12-24 hours. 
  4. Shaping Bagels: Remove the dough from the fridge and place it on a pastry mat (this makes it so easy to work with the dough, and you don’t have to flour your surface). Divide into seven pieces (weighing about 4 ounces), and form into balls. Slightly flatten them, and poke a hole in the middle with your finger. Stretch the hole a bit to widen. Place on a tray dusted with cornmeal and let them rise 30 minutes. 
  5. Boil the bagels—Preheat the oven to 400°F. Meanwhile, I fill my pot with 3-4 quarts of water and bring it to a boil. Then, I add 1 T each of baking soda and brown sugar. Drop the bagels in and cook for 30-40 seconds on each side. Remove the bagels with a slotted spoon and place them on a silicone-lined baking sheet.
  6. Sprinkle with additional cheese and jalapeno slices and bake for 20 minutes or until browned. 

Can Jalapeno Cheddar Sourdough Bagels Be Baked The Same Day? 

These sourdough bagels can be made and baked on the same day. However, they should be baked no longer than 7 hours after you make the dough. Keep the dough refrigerated for long fermentation so it doesn’t taste too sour. I like to keep it out for 4 hours to bulk ferment and then hide it in the fridge to bake the next morning. Long fermentation increases the bioavailability of nutrients in the grains. So, if you want the extra lactic acid, let it go overnight in the fridge. 

How To Store and Freeze Sourdough Bagels Made With Jalapenos, Cheddar, and Bacon. 

I store my jalapeño cheddar sourdough bagels in a plastic bread bag or Ziploc bag at room temperature. You can also store them covered with the dome of a cake stand.

It is not recommended to store sourdough bread in the fridge as it will become stiff.

Bagels can be frozen in a gallon freezer bag or airtight container for up to 3 months. Thaw entirely before toasting. 

Tips for Making Homemade Jalapeno Cheddar Bagels Using Freshly Milled Wheat:

  1. If refrigerating, allow the dough to sit at room temperature (about two hours) before shaping, and then let the bagels rest for 30 minutes before boiling. If you skip that extra rising, they will still be delicious. 
  2. This recipe works best with a fed starter. Feed your starter in the early morning to make the bagel dough at noon. I usually feed mine around 6:00 AM and start the dough around lunch.
  3. Don’t over-ferment at room temperature! Long-fermented sourdough bagels are best stored in the fridge and used within 2-3 days. If they sit on the counter too long (usually past 8 hours), the dough can release a liquid called lactic acid and become a sloppy mess to work with later. 
  4. I feed my sourdough starter with King Arthur flour. Using unbleached bread flour strengthens my starter.
  5. This dough is wetter than the typical stiff bagel dough, making it exceptionally soft and chewy! 
  6. If using pickled jalapeno peppers, drain the brine to avoid adding excess liquid to the dough. 
  7. Don’t use bacon bits, as the bacon grease also affects the dough. Fresh bacon adds so much flavor and takes minutes to cook for this recipe! 
  8. Garnish the tops lightly with cheddar cheese; you don’t want to overdo it. I like to cut my jalapeno slices in half to stretch them and not make them look too overpowering. 
  9. Bake these bagels the same day for quick and easy sourdough bagels. Begin your dough in the morning to get a head start and finish in the evening. 

Jalapeno Cheddar Sourdough Bagels with Freshly Milled Flour

Prep Time: 5 minutes
Cook Time: 20 minutes
Fermenting:: 16 hours
Total Time: 16 hours 25 minutes
Servings: 7 bagels
Chewy and flavorful sourdough bagels using only freshly milled flour! This bagel recipe is loaded with savory bacon, cheddar cheese, and jalapeno pieces. It isn't too spicy, and it makes the most delish and wholesome bagel for ham sandwiches! Even kids rave about how good these are! I share how easy it is to make these Jalapeno cheddar bagels with my step-by-step tutorial! 

Equipment

  • 1 heavy-duty stand mixer
  • 1 glass bowl with a lid
  • 1 18x13" sheet pan
  • 1 silicon mat

Ingredients

Ingredients:

  • 2/3 cup warm water
  • 1 cup active sourdough starter
  • 1 tsp honey
  • 289 grams hard white wheat  (freshly milled in a grain mill)
  • 2 Tbsp fresh jalapenos (or pickled, just drain)
  • 2 slices thick-cut bacon (chopped and fried; transfer and cool with the grease)
  • 1/4 cup cheddar cheese (shredded)
  • 3/4 tsp sea salt

For Boiling The Bagels:

  • 3 quarts water
  • 1 Tbsp brown sugar
  • 1 Tbsp baking soda

Topping:

  • 1 small jalapeno pepper (sliced into pieces)
  • 1/3 cup cheddar cheese (shredded)

Instructions

Directions:

  • jalapeno cheddar bagel dough with sourdough starter
    Add the water, sourdough starter, honey, freshly milled flour, chopped jalapenos, 1/4 cup cheddar cheese, and bacon with the grease to a stand mixer. Knead for 15-20 minutes until the dough is smooth and no longer sticks to the sides. Add the salt and continue to knead for five more minutes.
  • Transfer to a glass bowl and cover with a lid. Ferment dough for 4 hours at room tempertature and then place bowl into the fridge to cold ferment 12-24 hours. See notes below on how to make same-day bagels.
  • Shape the bagels by dividing the dough into seven equal pieces. Form each piece into a ball and poke a hole through the middle to make a bagel.
  • jalapeno cheddar bagelson a tray dusted with cornmeal
    Place bagels on a cornmeal-dusted tray and let them rise for 30 minutes.
  • Meanwhile, preheat the oven to 400°F. Bring the water to a boil and add the baking soda and brown sugar. Drop the bagels in, four at a time, and flip over to each side for 30-40 seconds. Transfer them to a silicone-lined baking sheet.
  • sourdough bagels topped with cheddar cheese and jalapenos
    Sprinkle the tops with 1 Tbsp of cheddar cheese and a few jalapeno pieces.
  • baked homemade jalapeno cheddar bagels using freshly milled flour
    Bake the bagels for 20-22 minutes or until golden brown.

Notes

  • For same-day bagels, make the dough and ferment it for 5-7 hours on the counter in a warm place. Shape and boil, then bake as directed. 
  • Weigh the hard white wheat berries using a scale, then run them through a grain mill to make whole wheat flour. 

Nutrition per serving

Serving: 1jalapeno cheddar bagelCalories: 227kcalCarbohydrates: 35gProtein: 9gFat: 7gSaturated Fat: 3gPolyunsaturated Fat: 1gMonounsaturated Fat: 2gTrans Fat: 0.01gCholesterol: 14mgSodium: 868mgPotassium: 193mgFiber: 5gSugar: 3gVitamin A: 168IUVitamin C: 7mgCalcium: 98mgIron: 2mg

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