Jalapeño Cheddar Sourdough Bagels

These jalapeño cheddar sourdough bagels are soft and chewy with melty cheese and just the right amount of jalapeño heat in every bite. Made with fresh jalapeños, grass-fed cheese, and the bagel is sourdough and naturally fermented, so it’s gut healthy and nutritious! 

The other week, while reminiscing about one of my all-time favorite game-day snacks, jalapeno poppers, an idea struck me – why not infuse those amazing ingredients into a bagel? The spicy kick of jalapenos with rich cheddar cheese, all wrapped up in a chewy sourdough bagel, sounded PERFECT. Inspired by jalapeno poppers: this is the best jalapeno cheddar sourdough bagel recipe. After some experimentation and many recipe tests, I think I figured it out.

These easy jalapeño cheddar sourdough bagels are bursting with peppery, cheesy flavor thanks to fresh jalapeños, raw grass-fed cheddar on the inside, and a generous heap of grated cheddar on top. My mouth is watering just thinking about it!

Why are sourdough bagels gut healthy and nutritious?

Sourdough bagels offer a plethora of gut-healthy benefits, thanks to their unique and natural fermentation process using sourdough starter. This slow and natural fermentation allows beneficial bacteria and wild yeast to work their magic, breaking down gluten and phytic acid, making the bagels easy to digest. As a result, nutrients like B vitamins, iron, and minerals become bio-available. The lower glycemic index of sourdough bagels ensures a steady and sustained release of energy (no energy crash!). With the addition of whole-grain flour, these bagels provide a nourishing blend of fiber, protein, and essential nutrients. But the goodness doesn’t end there – the fermentation process also synthesizes prebiotic fiber which promotes a healthy gut microbiome. All these benefits combined make sourdough bagels a delicious and nutritious food that supports overall well-being (and is one of my favorite ways to start the day!)

Bagel Recipe Ingredients

Here’s what you’ll need for this recipe:

The Dough

• Bread flour – Because of its high protein content, bread flour makes these homemade bagels delightfully chewy.
• Honey – Gives the bagels a hint of sweetness and adds to their soft texture.
• Water – Brings the dough together.
• Active sourdough starter – They couldn’t rise without it!
• Sea Salt – Enhances flavor (and nutrition) by slowing fermentation.
• Raw Cheddar Cheese – The star of the show!
• Fresh Jalapenos

Additional Ingredients

• Egg Wash: I think the egg wash adds an extra-delicious chew! However, you can also add the cheese directly to the boiled bagels.

Equipment Needed for Sourdough Bagels

• Dough Mixer or Mixing Bowl (by hand): You can prepare the bagel dough with either a mixer or by hand. Kneading the dough by hand is essential to the bagel-making process (and my favorite part!).
• Dough Scraper: Used for dividing our dough.
• Baking Pan
• Baking Scale: Ideal for accurately measuring ingredients and weighing bagel dough after dividing to ensure they are similar in size.

Why I Love Raw Cheese

Raw cheese is made from unpasteurized milk, so it has all those natural enzymes, probiotics, and good bacteria intact. These live cultures not only make raw cheese taste more flavorful, but they also aid in digestion and support a healthy gut microbiome. Raw cheese has a much higher concentration of essential nutrients like vitamins A, D, and K2, and minerals like calcium and magnesium. Plus, the natural enzymes found in raw cheese allow our bodies to easily absorb those nutrients too.

Are you new to making sourdough bagels?

Ready to learn how to make bagels? Check out this step-by-step guide first with visuals, and then find the full recipe at the bottom of this post!

Steps to Make Jalapeno Cheddar Sourdough Bagels

1. MIX DOUGH: In a stand mixer, add flour, sourdough starter, cheese chunks, water, honey, and salt. Place the dough hook on the mixer and mix the dough on the lowest speed for 3 minutes. By hand: In a bowl, add flour, sourdough starter, cheese chunks, water, honey, and salt. Mix by hand for a couple of minutes until a ball forms. Now, turn the dough onto a lightly floured surface and knead the dough for 3-4 minutes or until the dough looks smooth.
2. FIRST RISE / STRETCH AND FOLDS: Place dough in a tupperware and cover securely. Let the dough rise at room temperature for 6-8 hours or until it doubles in size. If you have the opportunity, stretch and fold your dough 3-4x during the first rise (ideally within the first few hours). To do this, stretch one side of the dough up and fold it all the way over to the other side. Then, rotate the bowl and continue on all four sides.
3. OVERNIGHT RISE: Place your dough covered in the fridge for an overnight rise. This is where your dough will develop flavor and L.A.B bacteria will get to work enhancing the nutrition of our dough.
4. DIVIDE AND SHAPE: The next day, dump out and divide your dough into 6-8 pieces, you can eyeball it or weigh out 80g-120g pieces. Shape each into a ball by pulling the corners up and over. Now, use your finger to poke a hole through the center of each ball and rotate the dough with two fingers to form a ring. Refer to visual.
5. FINAL (SHORT) RISE: Place your bagels in a greased tupperware and cover securely or a greased baking sheet and covered with plastic wrap. Make sure the bagels are covered tightly so the tops do not dry out. Let the bagels rise for 1-3 hours or until puffy to the touch. In the summer, this will take 2 hours and in the winter, it could take 3-4 hours.
6. BOIL BAGELS: Preheat oven to 400f. Fill a large, wide pot of water and bring to a boil. Drop bagels in, 1-2 at a time, making sure they have enough room to float around. Cook the bagels for 1 minute on each side and remove with a slotted spoon; drain well. Place on a baking sheet or plate and brush with egg wash.
7. Add Toppings: Top each bagel with shredded cheddar cheese.
8. BAKE: Bake bagels for 20-23 minutes or until golden brown on the outside.

Bagel Recipe Tips

• Weigh your ingredients. You should always weigh your ingredients using a baking scale! If you don’t have a kitchen scale, you can buy this one here on amazon.
• Let the dough rise somewhere warm. Sourdough starter and fermentation in general respond to warmth, so it’s always best to keep the dough somewhere warm (but covered and away from the sun)!
• Keep it covered. To keep the bagel dough moist, always cover it tightly with plastic wrap or with a lid. Cover all of it during each rise and any dough you’re not working with while you shape the bagels.
• It’s all in the final rise: During the final rise, this is where the magic happens. This final fermentation step allows are bagels to get soft and fluffy and can take anywhere from 1-3 hours depending on the temperature of your home. You know they’re ready when they feel puffy and feel aerated when poking with your finger or when they’ve almost doubled in size. You’ve gone too far if they’re hard to pick up without squishy or deflating. It can take several tries to get it right!

How to Top Your Jalapeno Cheddar Sourdough Bagels

I topped my bagel with a fresh chive and bacon cream cheese but this one would be great with butter, cream cheese, and other toppings like egg salad, or sliced avocado and eggs.

How to Store and Reheat Jalapeno Cheddar Sourdough Bagels

You can also reheat these the next day in a toaster oven for 5-10 minutes at 400f. To keep your homemade jalapeno cheddar bagels fresh, store them in an airtight container at room temperature for up to 3 days. If you want to keep them for longer, refrigerate or freeze them for up to 2 months, ensuring you can enjoy their deliciousness whenever you crave them.

QUESTION: What’s your favorite bagel flavor and what do you top it with?

If you make anything from SJ, be sure to tag me on Instagram — I love seeing your creations and featuring what you make! You can also find me on TikTok, Pinterest, or Youtube (@sourdoughjesha)!

More Favorite Bagel Recipes

If you love this bagel recipe, try one of these bagels next:

Mac and Cheese Sourdough Bagels

Everything Sourdough Bagels

Strawberry Shortcake Sourdough Bagels

Blueberry Sourdough Bagels

Pumpkin Sourdough Bagels

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