Gluten Free Pretzel Bagels (Sourdough Discard Recipe)

Gluten Free Pretzel Bagels are the best of both worlds. They combine the chewy, satisfying texture of my gluten free bagels with the salty, deep golden crust of my gluten free soft pretzels. Pretzel Bagels are incredibly versatile and can be served in many delicious ways. For a classic touch, enjoy them warm with a smear of cream cheese or butter. You could also pair them with mustard or cheese spreads for a savory option, just like a traditional soft pretzel.

Recipe Ingredients Notes

Super Fine Brown Rice Flour: This gluten free flour gives the pretzel bagels their structure. I recommend using super fine brown rice flour since regular ground brown rice flour will give the buns a gritty texture. I do NOT recommend using white rice flour since it is lower in protein and will cause a gummy texture in the dough.

Sorghum Flour: Sorghum flour is high in protein and has a soft texture with a light color. It gives the bagels a light, airy texture while adding depth of flavor. If needed, you can substitute it with millet, chickpea, or buckwheat flour (though buckwheat will result in darker bagels).

Potato Starch: Potato starch (which is not the same as potato flour!) helps lighten the crumb of gluten-free bagels. It’s made from the root tubers of potato plants.

Tapioca Starch/Flour: Tapioca starch/flour gives baked goods a chewy texture, as well as, contributes to the browning.

Whole Psyllium Husk: This ingredient helps to reduce the crumbly structure often found in gluten free baked goods. It also gives the dough a wheat-like texture. I only use Whole Psyllium Husks in my recipes.

Milk Powder: Milk Powder is an optional ingredient. The casein found in milk powder helps gluten-free bread to rise higher and have a lighter crumb. It also contributes to the color of bread or other baked goods.

Vinegar: The added vinegar activates sodium bicarbonate found in the baking powder which helps the pretzel bagels to rise. White Vinegar or Apple Cider Vinegar work in this recipe.

Gluten Free Sourdough Discard: Sourdough discard is a term used for the part of the gluten-free sourdough starter that is taken out and thrown away when it's being fed. For this gluten free artisan loaf recipe use unfed sourdough discard. This recipe calls for a 50:50 sourdough starter, equal parts gluten-free superfine brown rice flour and water. Discard must be at room temperature.

Food Grade Lye: Food-grade lye is what gives pretzel bagels their dark, shiny crust and special flavor. Also called sodium hydroxide (NaOH), lye is a strong alkaline substance used in food. It’s safe to eat when used in the right amount and handled carefully. Lye can be dangerous in its raw form, but once it’s diluted and the food is baked or cooked, it becomes safe to eat.

Recommended Tools

To successfully make this gluten free pretzel bagel recipe, you will need a few kitchen tools you most likely already have in your home.

• Digital Kitchen Scale: is a must-have to make this recipe (or any of my recipes). For small amounts under 10 grams, I like to use this Precision Pocket Scale.
• Stand Mixer: fitted with the dough hook will work the best to make this gluten free bread recipe. One can make the dough mixing it by hand but it will be sticky.
• Baking Sheets: two baking sheets, parchment paper. I prefer commercial half sheet pans since they are more durable.
• Water Spray Bottle: This is not mandatory but I like to have a water spray bottle on hand to give my gluten free bagels a little mist before proofing. I got mine at a local dollar discount store.
• Additional Tools: a nonreactive stainless steel bowl, a slotted spoon, a wooden spoon or plastic spoon to mix the lye and water with, latex gloves, eye protection (optional but recommended if it's your first time working with lye)

Why use food grade lye for Pretzel Bagel

I understand not everyone wants to use food grade lye in their kitchen but believe me when I say it will take your gluten free pretzels and pretzel bagels to the next level. Working with food grade lye is a lot quicker and easier than boiling bagels in a baking soda bath. Detailed instructions how to do a baking soda bath can be found here: Baking Soda Bath for Gluten Free Pretzels

• Authentic Flavor: Lye helps create the unique taste that traditional pretzels are known for. It adds a slightly nutty flavor that makes them more delicious.
• Shiny, Dark Crust: The alkaline nature of lye helps the pretzels develop a dark, glossy crust when baked. This is a signature look for classic pretzels.
• Chewy Texture: Lye contributes to the chewy texture that many people love in pretzels. It affects the dough’s protein structure, making each bite satisfying.
• Traditional Method: Using lye is part of the authentic Austrian and German pretzel-making process.

Gluten Free Pretzel Bagel Dough

I highly recommend using a stand mixer or an electric hand mixer to make the dough for gluten-free bagels. Mixing this by hand can be a workout. Plus gluten-free bread dough tends to be very sticky.

1. Start by warming the water in a small bowl in the microwave for 30-60 seconds until it reaches around 110°F. Ensure the temperature doesn’t go above 115°F, or it could kill the yeast. It’s a good idea to use a digital thermometer to check.
2. Sprinkle the active dry yeast and a pinch of sugar over the warmed water. Let it sit for 10-15 minutes. The yeast is ready when it looks bubbly and frothy. If it’s not bubbly after 10 minutes, it’s likely no longer active and shouldn’t be used.
3. In the bowl of a stand mixer with a dough hook attachment, combine the brown rice flour, sorghum flour, tapioca starch, potato starch, brown sugar, baking powder, milk powder (if using), kosher salt, psyllium husk, and xanthan gum. Whisk everything together.
4. Next, add the sourdough starter, oil, and vinegar to the dry ingredients.
5. When the yeast mixture is ready, pour it into the dry ingredients. Mix on low speed until combined, then increase the speed to medium-high and mix for 3-4 minutes. The dough will be soft, which is normal for gluten-free bread dough.
6. Allow the gluten pretzel bagel dough to rest in the bowl for 10 minutes. This gives the gluten free flours time to hydrate and become easier to handle.

Shaping & Proofing of Gluten Free Pretzel Bagels

During countless rounds of testing this pretzel bagel recipe, I realized it's a lot easier to shape the bagels on a lightly greased surface with highly greased hands than using additional flour. Make sure you start with a clean surface. I lightly spray mine with some non-stick cooking spray. You can also Oil Sprayer with some neutral oil like canola oil or vegetable oil.

1. Line a baking tray with parchment paper and lightly spray it with nonstick cooking spray. Set aside. If you skip spraying, the bagels will likely stick to the parchment paper.
2. Using a kitchen scale, divide the dough into five equal pieces by weight. Weigh the entire dough and divide by six. My portions typically weigh around 115 grams each.
3. Shape each piece into a tight ball, gently press it down and then carefully press your thumb into the center of each ball to form a hole, widening it to about 1 inch. Don’t worry if the hole seems large— the bagels will rise and the hole will shrink during baking. If the dough feels sticky, lightly grease your hands, which makes shaping easier.
4. Carefully transfer the shaped bagels to the prepared baking sheet, leaving enough space between them to rise.
5. Once all the bagels are shaped, cover them with a clean tea towel. Let the dough rise in a warm place until they are about 50% larger in size. I like to use my oven for this: preheat it briefly until it reaches around 100°F (be sure to check your oven thermometer!), then turn it off and place the tray of bagels inside. Depending on how warm your kitchen or proofing environment is, this can take 60 to 90 minutes. In warm, humid conditions, the bagels will proof more quickly.

Lye Bath and Baking

Once the gluten free pretzel bagels are puffy and about 50% larger than their original size, transfer the entire baking sheet to the freezer. Freezing the bagels for 10-15 minutes while you preheat the oven, prepare the lye bath, get some pretzel salt and gather your safety gear will make them easier to handle.

1. Preheat your oven to 425F and arrange your oven rack in the center of the oven.
2. In a well ventilated area set up your lye bath work station. If this is your first time working with lye, I recommend putting some newspaper or at least parchment paper on your kitchen counter to ensure the lye won't ruin the surface. Make sure to use a non reactive stainless steel bowl or a glass container like a pyrex pan. Have a plastic or metal spoon to mix the lye with the water handy. And please, make sure to wear gloves! (If you have curious kids or pets, now is the time to give them a little project in another room)
3. Start by lining your second baking sheet with parchment paper and generously spray it with non stick spray. This is the sheet pan you will use to bake the pretzel bagels on.
4. To prepare the lye solution, add 300 grams of COLD water to your container of choice.
5. Carefully add 12 grams of food-grade lye to the 300 grams cold water. This is a 4% solution. Always add lye to water, not the other way around, as adding water to lye can cause a dangerous reaction. Please measure correctly. This is not the time to "eye ball" things.
6. Stir the solution carefully until the lye is completely dissolved. The solution will heat up as the lye dissolves. (If you touch the outside of your container, you should feel it warm up)
7. Remove the bagels from the freezer and with a slotted spoon, carefully ONE bagel to the lye bath. Allow it to sit in the solution for about 15-20 seconds and then carefully turn it over. Always turn them away from you in case there are splatters.
8. Carefully remove the bagel from the lye bath and place it on the prepared sheet pan. Repeat with all the pretzel bagels.
9. Once all the bagels have been dipped in the lye bath, sprinkle them with some pretzel salt. Keep in mind that a little can go a long way with pretzel salt since it is very salty.
10. Bake the Gluten Free Pretzel Bagels for 18-20 minutes until dark golden brown. I highly recommend keeping an eye on them after 18 minutes since every oven is different. Their internal temperature should be around 200F.
11. Remove the baked gluten free bagels from the oven and allow them to cool on the baking pan for a few minutes before transferring them to a wire rack to cool completely.

Storing and Freezing

Gluten Free Pretzel Bagels, like bagels in general, are best enjoyed on the day they are baked. The longer they sit, the chewier they can become. Additionally, pretzels naturally contain moisture, which can cause the pretzel salt to dissolve. While gluten free bagels remain safe to eat and retain their salty flavor, this melting can lead to a wrinkled appearance and a slightly wet texture. I often skip the pretzel salt when making pretzel bagels for the freezer, and they’re still delicious without the topping.

To store the bagels, I recommend placing them in a brown paper bag at room temperature for up to two days. If you like, add a paper towel inside the bag to help absorb moisture. I suggest toasting them before enjoying to re-crisp the texture. Don't forget, you can always turn leftover bagels into delicious homemade gluten free bagel chips.

For freezing, ensure the bagels are fully cooled. Wrap each individual bagel in plastic wrap and place them in a ziplock bag or airtight container. Freeze up to 6 weeks. For easier thawing, consider slicing them before freezing, so you can pop them directly into your (gluten free) toaster.

FAQ - Gluten Free Pretzel Bagels

Note about Salt in my Recipes

I use Diamond Kosher Crystal Salt in all of my recipes unless otherwise stated. If use use a different brand or kind of salt in your kitchen please adjust accordingly since some salts can be saltier. If you use Morton’s Kosher Salt please be aware that their salt granules are smaller in size, denser, and crunchier and twice as salty.

Baking in grams

I share my recipes in grams and by weight since baking by weight is the most accurate way to bake. Digital Scales are very affordable and easy to use. You can purchase them on Amazon for less than a set of measuring cups. For small amounts under 10 grams, I like to use this Precision Pocket Scale. Measuring cups are very inaccurate which can cause significant errors when it comes to gluten-free baking or baking in general. Especially since I bake with gluten-free flours which weigh differently than “regular” flours. I do provide some ingredients like spices and leavening agents in measuring spoons. To learn more about Baking with a digital scale, make sure to check out my post about Baking by weight.

Note about Ovens and Oven Temperatures

All my recipes are tested and developed with a conventional oven. I always bake my baked goods on the rack placed in the MIDDLE of my oven. This way the heat coming from the bottom will not burn my baked goods.

If you are baking with convection (fan-forced), please adjust the recipes accordingly. Convection oven can cause baked goods to dry out quickly and still be raw inside. Since takes at least 15-20 minutes for a standard American Oven to be fully preheated. I highly recommend investing in an Oven Thermometer.

Substitutions and Modifications

Any dietary or ingredient modifications/substitutions to this recipe may alter the end result in appearance and taste. I test my recipes several times as published in this post and The Gluten Free Austrian Blog is not responsible for the outcome of any recipe you find on our website.