Best Sourdough Discard Protein Bagels

Finding a good use for your sourdough discard can feel impossible, especially when you’re tired of making the same pancakes or crackers week after week. And if you’re looking to add more protein to your breakfast routine without sacrificing that homemade bread taste you love, the options seem pretty limited.

That’s where these sourdough discard protein bagels come in handy: they put your extra starter to work, pack in way more protein than regular bagels thanks to Greek yogurt, and give you that chewy, satisfying texture you’d expect from a bakery-quality bagel.

SAVE NOW

What Kind of Sourdough Discard Should I Use?

Any sourdough discard will work for this recipe, whether it’s fresh from your morning feeding or something you’ve been storing in the fridge for a week or two. The discard doesn’t need to be active or bubbly since the yeast in the recipe is doing the heavy lifting for rise and texture. If your discard has been sitting in the fridge for a while, just give it a good stir before measuring it out to make sure any liquid (called hooch) is mixed back in. And don’t worry too much about whether your discard is 100% hydration or something different – a little variation won’t make or break your bagels.

SAVE NOW

Options for Substitutions

Here are some swaps you can make if you’re missing certain ingredients:

• Bread flour: All-purpose flour can work in place of bread flour, though your bagels might be slightly less chewy. You can also try a mix of 3 cups all-purpose flour and 1 cup whole wheat flour for added nutrition.
• Yogurt: Greek yogurt, regular yogurt, or even sour cream all work here. If you’re using Greek yogurt, thin it out with a tablespoon or two of water to match regular yogurt’s consistency.
• Sourdough discard: This is the star ingredient that gives these bagels their tangy flavor, so I wouldn’t recommend skipping it. If you don’t have exactly 200 grams, anywhere from 150-250 grams will work – just adjust the water slightly if your dough feels too dry or sticky.
• Everything bagel seasoning: Feel free to use sesame seeds, poppy seeds, sea salt, or any other bagel topping you prefer. You can also leave them plain or make a cinnamon-sugar version by swapping the savory toppings.
• Egg white: If you don’t want to waste the yolk, you can use a whole beaten egg for the wash, or substitute with a bit of milk or cream for shine.

Watch Out for These Mistakes While Baking

The biggest mistake when making bagels is skipping or rushing the boiling step, which is what gives bagels their signature chewy crust – make sure your water is at a rolling boil and don’t crowd the pot, as this drops the temperature and leads to dense, bread-like results instead of proper bagels.

Another common error is over-kneading the dough, which can make your bagels tough and hard to chew, so stick to the 4-5 minute kneading time and stop once the dough feels smooth and slightly tacky.

When shaping your bagels, avoid making the center hole too small since it will close up during boiling and baking – aim for a hole about 2 inches wide, which might look too big at first but will shrink to the perfect size.

Finally, don’t overbake them just because they don’t look golden enough at 18 minutes, as bagels continue to firm up as they cool and leaving them in too long will result in rock-hard bagels that are difficult to slice.

SAVE NOW

What to Serve With Sourdough Discard Protein Bagels?

These bagels are perfect for a weekend breakfast spread with all your favorite toppings laid out. I love toasting mine and slathering on cream cheese with smoked salmon, red onion, and capers for a classic bagel shop experience at home. If you’re keeping things simple, try them with plain cream cheese, butter and jam, or even peanut butter and banana for a filling breakfast. They also make great sandwich bagels – just slice them in half and fill with scrambled eggs, bacon, and cheese for a hearty breakfast sandwich that’ll keep you going all morning.

Storage Instructions

Store: Once your bagels have cooled completely, keep them in an airtight container or zip-top bag at room temperature for up to 3 days. If you want them to last a bit longer, store them in the fridge for up to a week, though they might lose a little of that fresh-baked chewiness.

Freeze: Bagels are perfect for freezing! Slice them in half first (makes toasting so much easier later), then wrap each one individually in plastic wrap or foil before placing them all in a freezer bag. They’ll keep for up to 3 months this way.

Toast: For room temp or refrigerated bagels, just slice and toast as usual. If you’re working with frozen ones, you can pop them straight into the toaster from the freezer – no need to thaw first. They’ll taste almost as good as fresh from the oven!

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 1500-1700
• Protein: 50-60 g
• Fat: 15-20 g
• Carbohydrates: 300-330 g

Ingredients

For the dough:

• 0.75 cup water (luke-warm, ideally between 100°F and 110°F)
• 1 tsp sugar
• 1.5 tsp yeast (I find Red Star Active Dry gives the most consistent rise)
• 4.25 cups bread flour (I always use King Arthur for the high protein content)
• 1 cup yogurt (Fage non-fat Greek yogurt adds great protein and tang)
• 7 oz sourdough discard
• 2.5 tsp salt
• 0.5 tsp onion powder

For the boiling water:

• 2 tbsp sugar

For the topping:

• 1 egg white
• 1 tbsp water
• everything bagel seasoning

Step 1: Activate the Yeast and Prepare the Dough Base

• 0.75 cup water
• 1 tsp sugar
• 1.5 tsp yeast

In a small bowl, combine the lukewarm water (100-110°F), 1 teaspoon of sugar, and yeast.

Let this mixture sit undisturbed for 5 minutes until it becomes foamy on top—this bloom confirms your yeast is alive and active.

While the yeast activates, measure out your bread flour, yogurt, sourdough discard, salt, and onion powder into a large mixing bowl.

Step 2: Mix and Develop the Bagel Dough

• yeast bloom from Step 1
• 4.25 cups bread flour
• 1 cup yogurt
• 7 oz sourdough discard
• 2.5 tsp salt
• 0.5 tsp onion powder

Pour the activated yeast mixture into your bowl of dry ingredients.

Add the yogurt and sourdough discard, then stir everything together until a shaggy dough forms.

Transfer to a lightly floured surface and knead for 4-5 minutes until the dough becomes smooth, elastic, and slightly tacky.

I like to knead by hand here because you can really feel when the gluten develops and the dough reaches the right texture—it should resist slightly when you push it but spring back quickly.

Step 3: First Rise

• kneaded dough from Step 2

Place the kneaded dough from Step 2 into a lightly greased bowl, turning it over once to coat lightly with oil.

Cover loosely with plastic wrap or a damp towel and let it rise at room temperature for 90 minutes until it roughly doubles in size.

This long, slow rise develops flavor from the sourdough discard and creates a more complex taste than quick bagels.

Step 4: Shape the Bagels

• risen dough from Step 3

Turn the risen dough onto a lightly floured surface and divide it into 8-10 equal pieces (I find 9 pieces gives a nice medium-sized bagel).

Roll each piece into a tight ball, then poke your thumb through the center and gently stretch to form a bagel shape with a hole about 2 inches in diameter.

This allows the bagel to cook evenly and develop that signature chewy texture.

Place each formed bagel on a parchment-lined baking sheet, cover loosely, and let rest for 20 minutes.

Step 5: Prepare for Boiling and Baking

• 2 tbsp sugar
• 1 egg white
• 1 tbsp water

While the bagels rest, preheat your oven to 425°F and fill a large pot with 2 quarts of water.

Bring the water to a boil and stir in 2 tablespoons of sugar—this creates a gentle boil that helps set the bagel’s crust.

In a small bowl, whisk together the egg white and 1 tablespoon of water to create your egg wash for topping.

Step 6: Boil and Finish the Bagels

• rested bagels from Step 4
• egg wash from Step 5
• everything bagel seasoning

Carefully transfer each rested bagel from Step 4 into the boiling water, working in batches to avoid crowding the pot.

Boil for 20-30 seconds per side—you’ll see them float and then sink slightly back down, which signals they’re ready to flip.

Remove with a slotted spoon and place directly onto a baking sheet lined with parchment.

Brush each bagel generously with the egg wash from Step 5 and sprinkle with everything bagel seasoning while still slightly wet so it adheres well.

Step 7: Bake Until Golden and Serve

• prepared bagels from Step 6

Place the seasoned bagels in the preheated 425°F oven and bake for 18-22 minutes until they’re deep golden brown on the outside and sound hollow when tapped on the bottom.

The high protein flour and yogurt create a denser, chewier bagel that toasts beautifully.

Let cool on a wire rack for at least 10 minutes before slicing—this lets the crumb set properly so you get clean, defined slices.

Best Sourdough Discard Protein Bagels

Delicious Best Sourdough Discard Protein Bagels recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 1 hour hr 10 minutes mins

Cook Time 2 hours hrs 20 minutes mins

Total Time 3 hours hrs 32 minutes mins

Servings 8 bagels

Calories 1600 kcal

Ingredients

  

For the dough::

• 0.75 cup water (luke-warm, ideally between 100°F and 110°F)
• 1 tsp sugar
• 1.5 tsp yeast (I find Red Star Active Dry gives the most consistent rise)
• 4.25 cups bread flour (I always use King Arthur for the high protein content)
• 1 cup yogurt (Fage non-fat Greek yogurt adds great protein and tang)
• 7 oz sourdough discard
• 2.5 tsp salt
• 0.5 tsp onion powder

For the boiling water::

• 2 tbsp sugar

For the topping::

• 1 egg white
• 1 tbsp water
• everything bagel seasoning

Instructions

 

• In a small bowl, combine the lukewarm water (100-110°F), 1 teaspoon of sugar, and yeast. Let this mixture sit undisturbed for 5 minutes until it becomes foamy on top—this bloom confirms your yeast is alive and active. While the yeast activates, measure out your bread flour, yogurt, sourdough discard, salt, and onion powder into a large mixing bowl.
• Pour the activated yeast mixture into your bowl of dry ingredients. Add the yogurt and sourdough discard, then stir everything together until a shaggy dough forms. Transfer to a lightly floured surface and knead for 4-5 minutes until the dough becomes smooth, elastic, and slightly tacky. I like to knead by hand here because you can really feel when the gluten develops and the dough reaches the right texture—it should resist slightly when you push it but spring back quickly.
• Place the kneaded dough from Step 2 into a lightly greased bowl, turning it over once to coat lightly with oil. Cover loosely with plastic wrap or a damp towel and let it rise at room temperature for 90 minutes until it roughly doubles in size. This long, slow rise develops flavor from the sourdough discard and creates a more complex taste than quick bagels.
• Turn the risen dough onto a lightly floured surface and divide it into 8-10 equal pieces (I find 9 pieces gives a nice medium-sized bagel). Roll each piece into a tight ball, then poke your thumb through the center and gently stretch to form a bagel shape with a hole about 2 inches in diameter. This allows the bagel to cook evenly and develop that signature chewy texture. Place each formed bagel on a parchment-lined baking sheet, cover loosely, and let rest for 20 minutes.
• While the bagels rest, preheat your oven to 425°F and fill a large pot with 2 quarts of water. Bring the water to a boil and stir in 2 tablespoons of sugar—this creates a gentle boil that helps set the bagel's crust. In a small bowl, whisk together the egg white and 1 tablespoon of water to create your egg wash for topping.
• Carefully transfer each rested bagel from Step 4 into the boiling water, working in batches to avoid crowding the pot. Boil for 20-30 seconds per side—you'll see them float and then sink slightly back down, which signals they're ready to flip. Remove with a slotted spoon and place directly onto a baking sheet lined with parchment. Brush each bagel generously with the egg wash from Step 5 and sprinkle with everything bagel seasoning while still slightly wet so it adheres well.
• Place the seasoned bagels in the preheated 425°F oven and bake for 18-22 minutes until they're deep golden brown on the outside and sound hollow when tapped on the bottom. The high protein flour and yogurt create a denser, chewier bagel that toasts beautifully. Let cool on a wire rack for at least 10 minutes before slicing—this lets the crumb set properly so you get clean, defined slices.