There’s nothing sadder than mixing up a perfect sourdough bagel dough, tossing in your cheese and jalapeños, and watching the whole thing rip apart like a bad movie plot. Folding mix-ins into sourdough dough can feel tricky, but it doesn’t have to be. By using a few clever techniques, you can incorporate all that spicy, cheesy flavor without ruining your dough.

1. Start With Strong Dough

Before you even touch the cheese or jalapeños, make sure your sourdough bagel dough has some strength. Perform several stretch-and-fold techniques during bulk fermentation to develop gluten. A strong dough holds mix-ins way better and won’t tear like a weak one. Think of it as building a stretchy net to catch all that flavor.

2. Prep Your Mix-Ins Smartly

Cut your jalapeños into small, even pieces. If you’re using fresh ones, pat them dry so they don’t add too much moisture. For cheese, go with small cubes or shreds. Big chunks are more likely to poke holes in the dough. For gooey, melty pockets, avoid pre-shredded cheese and grate your own.

3. Add During the Right Stage

The best time to fold in jalapeños and cheese is after the first rest, when your dough is hydrated but not fully fermented. This way, the dough is pliable enough to absorb the mix-ins without fighting you, and it still has plenty of time to develop strength afterward.

4. Gentle Layering Is Key

Instead of dumping everything in at once and kneading aggressively, try this: flatten the dough slightly into a rough rectangle, sprinkle some of your cheese and jalapeños, fold it over, add more, and fold again. Think lasagna layering, but with dough. This spreads the mix-ins without forcing them through the dough like tiny wrecking balls.

5. Keep It Cool

If your cheese starts to melt into the dough while you’re folding, things get messy fast. Keep the cheese chilled until the last minute. Cold cheese is easier to work with and stays in nice little pockets while baking.

6. Don’t Panic Over Small Tears

Even if you’re careful, you might see a few little tears. It’s okay! Just pinch them closed gently and move on. Once the dough proofs and bakes, those tiny spots will seal right up, leaving you with beautiful sourdough bagels stuffed with jalapeños and cheddar.

Final Thoughts

Folding cheese and jalapeños into sourdough bagel dough doesn’t have to be stressful. Build a strong base, prep your mix-ins smart, and fold gently in layers. You’ll end up with perfectly chewy bagels studded with melty cheddar and spicy bites in every single piece. And honestly, once you bite into one, no one’s going to care how “perfect” your folds were anyway.

Ready to try it out?
Use these tips with our Easy Jalapeño Cheddar Sourdough Bagels recipe and load up on flavor without ruining your dough.