Sourdough Jalapeño & Cheddar-Filled Soft Pretzels

If you loved my sourdough pretzel recipe and you’re a fan of spicy food, you’re going to love this version! These Sourdough Jalapeño and Cheddar-Stuffed Soft Pretzels are filled with shredded sharp cheddar cheese and diced fresh jalapeños. Top them with some sliced jalapeños and more melty cheddar cheese for the best snack!

I’ve been dreaming up this recipe for a while now! Football Sunday season is officially here, and it’s so fun to have some new appetizers to enjoy while watching the game.

I love these sourdough jalapeno cheddar pretzels with honey mustard sauce (the spice from the fresh jalapenos and sweet tanginess of the honey mustard complement each other beautifully). Though I will say my beer cheese sauce is top-notch.

You’re going to love these pretzels–and how fun that they are naturally fermented and 100% sourdough!

More Sourdough Bakes!

• sourdough maple pecan bread
• sourdough fry bread
• sourdough focaccia bread
• soft sourdough sandwich bread

Why You’ll Love This Recipe

• Soft, chewy, and packed with flavor: Sourdough fermentation gives these pretzels an incredible texture and delicious depth of flavor. This is a 100% sourdough recipe!
• Gooey jalapeño cheddar filling: Every pretzel is stuffed with melty cheddar and fresh jalapeños for the perfect combination of cheesy, savory, and spicy. Absolute best game day appetizer (I love dipping them in a simple honey mustard sauce).
• Perfect for sharing: These homemade pretzels make an amazing snack, appetizer, or party treat—and they’re even better served warm with your favorite dipping sauce.

Step-By-Step Instructions

Add the sourdough starter, water, brown sugar, flour, and salt to the bowl of a stand mixer. Knead with the dough hook until a shaggy dough forms, then add the softened butter. Knead on medium-high for about 7 minutes, until smooth and elastic.

Place the dough in a lightly greased bowl, cover, and let rise at room temperature for 4–6 hours, or until it has increased by at least 50% in size.

Cover the dough and refrigerate for 8–24 hours.

Line a baking sheet with parchment and prepare 8 small parchment squares. Divide the chilled dough into 8 equal portions.

Roll each piece into a 20–24-inch rope, then flatten it to about 2 inches wide. Add shredded cheddar and diced jalapeños down the center, leaving room around the edges.

Pinch the dough firmly closed over the filling, then gently roll it back into a rope. Shape into a classic pretzel and place on an individual parchment square.

Pinch the seams together. Then roll it back into a rope.

Form the rope into a wide U shape, with the two ends pointing upward. Cross the ends over one another, then twist them twice.

Bring the twisted ends down toward the bottom of the U and press them gently onto the dough to secure the classic pretzel shape.

Cover the shaped pretzels and let them rise for 1–3 hours, or until noticeably puffy.

Preheat the oven to 400°F (204°C). Bring the water, baking soda, and brown sugar to a gentle boil in a large pot.

Working in batches, boil each pretzel for 30–40 seconds per side. Remove with a slotted spoon and place on a parchment-lined baking sheet.

Brush each pretzel generously with egg wash and sprinkle with coarse salt. Add sliced jalapeños to the tops.

Bake at 400°F (204°C) for about 18 minutes. Sprinkle the remaining shredded cheddar over the pretzels and return to the oven for 5 minutes, or until deeply golden and the cheese is melted and bubbly.

Let the pretzels cool for a few minutes before serving. Enjoy warm with your favorite dipping sauce.

Helpful Tips for the Best Sourdough Pretzels

• Use an active sourdough starter. For the best rise and texture, make sure your starter is bubbly, active, and at or near its peak when you mix the dough.
• Don’t rush the fermentation. Sourdough pretzels develop their best flavor when given enough time to ferment. Let the dough rise until it has increased by at least 50% before moving it to the refrigerator for the overnight cold ferment.
• Keep the dough cool when shaping. Chilled dough is much easier to roll, stuff, and shape. If it becomes too soft or sticky while you’re working, place it in the refrigerator for 10–15 minutes.
• Don’t overfill the pretzels. It can be tempting to add lots of cheese and jalapeños, but too much filling can make the dough difficult to seal and cause the cheese to leak during the baking soda bath.
• Seal the filling completely. After adding the cheddar and diced jalapeños, pinch the seam firmly closed along the entire length of the dough. A good seal keeps the filling tucked inside while the pretzels boil and bake.
• Leave room around the filling. When flattening the dough, keep a little space along the edges so you have enough dough to pinch together and create a secure seal.
• Use individual parchment squares. Placing each shaped pretzel on its own small piece of parchment makes transferring them into the baking soda bath much easier and helps prevent the delicate pretzel shape from getting distorted.
• Don’t skip the baking soda bath. This step gives pretzels their classic deep brown color, chewy exterior, and distinctive pretzel flavor. Make sure the water is gently boiling before adding the pretzels.
• Don’t overcrowd the pot. Boil only 2–3 pretzels at a time so they have enough room to cook evenly and are easy to flip and remove.
• Be generous with the egg wash. A thorough coating helps the pretzels develop that beautiful glossy, deep golden-brown crust.
• Adjust the jalapeños to your taste. Remove the seeds and membranes for a milder pretzel, or leave some intact if you want more heat. You can also add extra sliced jalapeños on top for a stronger jalapeño flavor.
• Let them cool briefly before eating. The melted cheese inside will be extremely hot when the pretzels first come out of the oven. Let them cool for several minutes before serving.
• Serve them warm. These pretzels are at their best shortly after baking, when the exterior is chewy and the cheddar filling is still warm and gooey.

Equipment

• Stand mixer with dough hook attachment
• Large mixing bowl
• Kitchen scale
• Large pot or Dutch oven for the baking soda bath
• Slotted spoon or spider strainer
• Large baking sheet
• Parchment paper
• Small bowls for the egg wash and filling
• Pastry brush
• Sharp knife or kitchen shears for slicing jalapeños
• Wire cooling rack, optional

Storage

• Room temperature: Store cooled pretzels in an airtight container or zip-top bag at room temperature for up to 2 days.
• Refrigerator: Refrigeration can make the pretzels a little firm, but they can be stored in an airtight container for up to 4 days.
• Freezer: For longer storage, wrap each cooled pretzel individually in plastic wrap or foil and place them in a freezer-safe bag for up to 3 months.
• Reheating: For the best texture, reheat refrigerated or frozen pretzels in a 350°F (175°C) oven or air fryer until warmed through. If frozen, there’s no need to thaw them first.

Sourdough Jalapeño & Cheddar-Filled Soft Pretzels

These sourdough jalapeño cheddar stuffed soft pretzels are soft, chewy, and golden brown with gooey cheddar and diced jalapeños tucked inside every bite. Topped with more melted cheese and fresh jalapeño slices, they’re the perfect savory sourdough treat for snacking, parties, or serving with your favorite dipping sauce.

5 from 1 vote

Print Pin Rate

Course: Sourdough

Cuisine: German

Prep Time: 30 minutes minutes

Cook Time: 23 minutes minutes

Bulk Fermentation: 15 hours hours

Total Time: 15 hours hours 23 minutes minutes

Servings: 8 stuffed pretzels

Author: Jamie

Ingredients

Sourdough Pretzel Dough

• ▢ 120 g active sourdough starter 1/2 cup, bubbly and at peak activity
• ▢ 240 g water 1 cup, room temperature
• ▢ 36 g brown sugar 3 tablespoons
• ▢ 420 g bread flour 3 1/2 cups
• ▢ 6 g salt 1 teaspoon
• ▢ 28 g salted butter 2 tablespoons, softened
• ▢ 14 g extra virgin olive oil 1 tablespoon, for greasing the bowl and plastic wrap

Jalapeño Cheddar Filling

• ▢ 170 g shredded cheddar cheese 1 cup
• ▢ 4 fresh jalapeños finely diced

Topping

• ▢ 170 g shredded cheddar cheese 1 cup
• ▢ 3 fresh jalapeños thinly sliced

Baking Soda Bath

• ▢ 7 cups water 1.65 L
• ▢ 1/4 cup baking soda 60 g
• ▢ 2 tablespoons brown sugar 24 g

Egg Wash

• ▢ 1 large egg whisked
• ▢ 1 teaspoon milk

Instructions

Mix and Knead the Dough

• In the bowl of a stand mixer, combine the active sourdough starter, water, brown sugar, bread flour, and salt. Using the dough hook attachment, knead on medium speed until the ingredients come together into a shaggy dough.
• Add the softened butter and continue kneading. Increase the mixer speed to medium-high and knead for about 7 minutes, or until the dough is smooth, elastic, and soft.
• If you don’t have a stand mixer, mix the ingredients together in a large bowl, then transfer the dough to a clean work surface and knead by hand for about 10–12 minutes.
• The finished dough should feel soft and slightly tacky but should not be excessively sticky. If the dough sticks heavily to your hands or work surface, add flour 1 tablespoon at a time until it becomes easier to handle.

First Rise

• Lightly grease a medium bowl with olive oil and place the dough inside. Cover with greased plastic wrap or a damp kitchen towel.
• Allow the dough to rise at room temperature for about 4–6 hours, depending on the temperature of your kitchen. The dough should increase in volume by at least 50% and can rise to nearly double in size.
• Because this is sourdough, fermentation time will vary depending on the strength of your starter and the temperature of your kitchen. Watch the dough rather than relying solely on the clock.

Cold Ferment Overnight

• Once the dough has completed its first rise, cover the bowl tightly and transfer it to the refrigerator.
• Refrigerate for 8–24 hours. The cold fermentation develops the sourdough flavor and makes the dough easier to handle and shape.

Prepare the Filling and Baking Sheet

• The next day, line a large baking sheet with parchment paper. Cut 8 small squares of parchment paper, one for each pretzel.
• Dice the jalapeños and shred the sharp cheddar cheese. When I prepare the jalapeños, I remove the seeds and membranes (you can keep the seeds for an extra kick!). I keep the seeds when I slice the jalapeños that I'll be adding on top of the pretzels.
• Keep the sliced jalapeños and the additional shredded cheddar separate. These will be used to top the pretzels later.
• Remove the dough from the refrigerator and divide it into 8 equal portions. Each piece should weigh approximately 100–110 g, depending on the total weight of your dough.
• Using a kitchen scale will help ensure all of your pretzels are the same size and bake evenly.

Stuff and Shape the Pretzels

• Work with one piece of dough at a time, keeping the remaining dough covered so it doesn’t dry out.
• Roll the dough into a long rope approximately 20 inches long.
• Instead of leaving the rope round, gently flatten the dough along its length until it is about 2 inches wide. You want enough surface area to add the filling while still leaving enough dough around the edges to seal it securely.
• Sprinkle approximately 1/8 of the cheddar and jalapeño filling down the center of the flattened dough, leaving a little room around the edges.
• Bring the long edges of the dough together and pinch the seam firmly closed, completely enclosing the cheese and jalapeños inside the dough. Check the entire seam carefully and pinch any areas that aren’t fully sealed.
• Gently roll the stuffed dough back into a rope, being careful not to squeeze out the filling.
• Form the rope into a large U shape. Cross the two ends over one another, twist them twice, then fold the twisted ends down toward the bottom of the U. Gently press the ends onto the base of the pretzel to secure the shape.
• Place the finished pretzel onto one of the individual parchment squares.
• Repeat with the remaining 7 pieces of dough.
• Tip: If the dough becomes warm, soft, or difficult to work with, place it back in the refrigerator for 10–15 minutes. Chilled dough is much easier to roll, fill, seal, and shape.

Second Rise

• Arrange the 8 shaped pretzels on a parchment-lined baking sheet, keeping each pretzel on its individual parchment square.
• Loosely cover the pretzels with greased plastic wrap and allow them to rise for about 1-3 hours, or until they look noticeably puffier.
• The exact time will depend on the temperature of your kitchen. You don’t want them to become extremely puffy; they should simply look lighter and slightly expanded.

Prepare the Baking Soda Bath

• When the pretzels are nearly finished with their second rise, preheat the oven to 204°C (400°F).
• Add the water, baking soda, and brown sugar to a large, wide pot. Bring the mixture to a gentle boil over medium-high heat.

Boil the Pretzels

• Carefully lift each pretzel using its parchment square and gently lower it into the baking soda bath. After a few seconds, carefully remove the parchment. It should slide away easily.
• Boil the pretzels for 30–40 seconds per side. Work in batches of 2–3 pretzels at a time so you don’t overcrowd the pot.
• Use a slotted spoon or spider strainer to carefully flip the pretzels and remove them from the water. If a pretzel sinks slightly, gently nudge it and it should float back toward the surface.
• Transfer the boiled pretzels to a parchment-lined baking sheet.

Add the Egg Wash and Jalapeños

• Whisk the egg and milk in a small bowl.
• Brush each pretzel generously with the egg wash, making sure to coat the exposed dough.
• Arrange several slices of fresh jalapeño over the top of each pretzel, gently pressing them into the egg wash so they stay in place during baking.

Bake

• Bake the pretzels at 204°C (400°F) for about 20-25 minutes total. About 5 minutes before they are finished baking (around the 18 minute mark), remove the pan from the oven and generously sprinkle the remaining shredded cheddar cheese over the tops of the pretzels.
• Return the pretzels to the oven and continue baking for approximately 5 minutes, or until the cheese is melted and bubbly and the pretzels are deeply golden brown.
• If necessary, rotate the baking sheet halfway through baking to encourage even browning. You may need to place these pretzels on two baking sheets. You can rotate the pans halfway through as well.

Cool and Serve

• Allow the pretzels to cool for several minutes before serving. The cheese filling will be extremely hot straight from the oven, so give them a little time to cool before biting into them.
• These pretzels are best served warm while the cheddar filling is still gooey and melty.
• Serve them on their own or with your favorite dipping sauce. They are especially delicious with beer cheese, queso, honey mustard, ranch, or a creamy jalapeño dipping sauce.

Nutrition

Serving: 1pretzel | Calories: 458kcal | Carbohydrates: 50g | Protein: 18g | Fat: 21g | Saturated Fat: 11g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 0.1g | Cholesterol: 73mg | Sodium: 1861mg | Potassium: 131mg | Fiber: 2g | Sugar: 8g | Vitamin A: 772IU | Vitamin C: 1mg | Calcium: 330mg | Iron: 1mg

Calories: 458kcal

Tried this recipe?Mention @Bake.With.Jamie