Everything Bagel You’ll Love, Easy, Homemade & High Protein

These protein everything bagels bake up chewy, golden, and boldly seasoned with sesame, poppy, onion, and garlic. Choose the classic version or boost each bagel with up to 16g of protein using one simple swap, Greek yogurt, whey isolate, or cottage cheese.

I’ve burned toast. I’ve forgotten yeast. And once? I made a bagel so dense my daughter used it as a hockey puck. But that’s exactly why I trust this recipe, it works. Whether you’re baking for a lazy Sunday or meal-prepping breakfast for the week, this one bends to your rhythm and your protein needs.

Let’s make a bagel that fits your life, not the other way around.

Everything Bagel You’ll Love, Easy, Homemade & High Protein

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• Author: Betty Thompson
• Total Time: 3 hours
• Yield: 8 bagels 1x
• Diet: Vegetarian

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Description

Here’s a complete recipe and tutorial for hot & fresh homemade everything bagels. Skip the store-bought and bakery because bagels are easier than you think! Don’t skip the water bath and egg wash, both provide that chewy texture and golden crust. Includes optional high-protein variations.

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Ingredients

Scale 1x2x3x

1 and 1/2 cups (360ml) warm water (100–110°F, 38–43°C)

2 and 3/4 teaspoons instant or active dry yeast

4 cups (520g) bread flour (spooned & leveled)

1 tablespoon packed light or dark brown sugar (or barley malt syrup)

2 teaspoons salt

Water Bath:

2 quarts water

1/4 cup (85g) honey (or barley malt syrup)

Topping:

2 tablespoons poppy seeds

2 tablespoons sesame seeds

1 tablespoon dried minced onion

1 tablespoon dried garlic flakes

1 tablespoon coarse or flaky sea salt

1 egg white beaten with 1 tablespoon water

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Instructions

1. Whisk warm water and yeast together in the bowl of a stand mixer fitted with a dough hook. Let sit for 5 minutes.

2. Add flour, brown sugar, and salt. Beat on low speed for 2 minutes.

3. Knead the dough in mixer or by hand for 6–7 minutes until smooth and slightly tacky.

4. Grease a large bowl, place the dough inside, turn to coat, and cover. Let rise 60–90 minutes until doubled.

5. Punch down dough. Divide into 8 pieces. Shape into balls, then poke holes and stretch into bagels.

6. Preheat oven to 425°F (218°C). Line 2 baking sheets with parchment.

7. Bring water and honey to a boil. Boil bagels 1 minute per side in batches.

8. Brush with egg wash, dip in topping mix, and place on baking sheets.

9. Bake for 20–25 minutes until golden brown, rotating pans halfway through.

10. Cool on sheet 20 minutes, then transfer to wire rack. Enjoy fresh or store/freeze for later.

Notes

Protein Variation: For a high-protein bagel, swap 1 cup bread flour with whey isolate OR add 1/2 cup blended cottage cheese or Greek yogurt while reducing water slightly. Adds approx. 5–7g protein per bagel.

Freezing Tip: Slice before freezing for easier toasting.

Make Ahead: Let dough rise overnight in the fridge for deeper flavor.

• Prep Time: 2 hours 10 minutes
• Cook Time: 25 minutes
• Category: Breakfast
• Method: Baking
• Cuisine: American

Nutrition

• Serving Size: 1 bagel
• Calories: 260
• Sugar: 2g
• Sodium: 480mg
• Fat: 1g
• Saturated Fat: 0g
• Unsaturated Fat: 1g
• Trans Fat: 0g
• Carbohydrates: 49g
• Fiber: 2g
• Protein: 9g
• Cholesterol: 0mg

The Power of the Custom Everything Bagel: Classic or Protein-Packed

What makes a protein bagel worth it?

Some mornings need more than carbs. That’s when a protein bagel steps in. By default, these bagels use bread flour, which already gives you a better chew and naturally higher protein (13–14% vs. all-purpose’s 8–10%). But if you’re looking for more fuel, something to carry you through workouts, meetings, or kid chaos, you’ve got options.

This recipe lets you keep it classic, or power it up with easy add-ins like:

• Plain whey isolate (for zero-flavor disruption)
• Greek yogurt (for moisture and protein)
• Cottage cheese (as in these cottage cheese bagels)

The result? A chewy, golden bagel you can adapt based on your needs. No more having to choose between functional food and comfort food.

Homemade bagels, your way (yes, even with protein)

I start with a tried-and-true method, yes, we boil and egg wash for that golden, chewy crust. The base gives you that classic New York-style flavor, but if you need more staying power (like I do most mornings), check out Part 2 for protein add-ins that blend right in.

If you’re pairing this with bagel topping ideas or a protein snack like banana protein muffins, you’ll have a high protein breakfast lineup that’s anything but boring.

How to Make Everything Bagels (With Optional Protein Boost)

This is the bagel that brought bakery flavor home, golden, chewy, and perfectly seasoned. It’s your go-to classic, with one optional twist: a protein add-in that fits your lifestyle. Follow the base exactly, or add the swaps below to make it a satisfying high protein bagel without sacrificing flavor.

Ingredients

Dough Base

• 1 and 1/2 cups (360ml) warm water (100–110°F, 38–43°C)
• 2 and 3/4 teaspoons instant or active dry yeast
• 4 cups (520g) bread flour (spooned & leveled)
• 1 tablespoon packed light or dark brown sugar (or barley malt syrup)
• 2 teaspoons salt

Water Bath

• 2 quarts water
• 1/4 cup (85g) honey (or barley malt syrup)

Topping

• 2 tablespoons poppy seeds
• 2 tablespoons sesame seeds
• 1 tablespoon dried minced onion
• 1 tablespoon dried garlic flakes
• 1 tablespoon coarse or flaky sea salt
• Egg wash: 1 egg white beaten with 1 tablespoon water

Optional Protein Add-Ins (Choose One)

Want to give your everything bagels a protein boost? Just one ingredient tweak adds 4 to 7 extra grams of protein per bagel, without losing that chewy, golden crust you love. I’ve tested these in my own kitchen (and yes, floured my glasses more than once). Each swap works with the same base dough, no fancy tools needed.

🔁 Whey Protein Isolate (Unflavored)

Use: 1 cup
Swap: Replace 1 cup of bread flour
Boost: +6–7g protein per bagel
Texture: Same chew, zero flavor change

🔁 Blended Cottage Cheese

Use: ½ cup (blend smooth)
Swap: Reduce water to 1¼ cups
Boost: +4–5g protein per bagel
Texture: Slightly softer, pillowy crumb

🔁 Plain Greek Yogurt (2% or Nonfat)

Use: ½ cup
Swap: Reduce water slightly (start slow)
Boost: +5g protein per bagel
Texture: Moist, mild tang

Want to go even bigger?

Combine whey and yogurt (or cottage cheese) for up to +10g protein per bagel, but only if you’re comfy handling stickier dough. If you’re new to baking, start with one swap, trust me, your dough will thank you.

Looking to round out your high-protein mornings? Try pairing these with our fresh milled protein muffins or chocolate chip protein muffins for a breakfast that sticks with you long past 10 a.m.

Step by Step

Step 1: Make the Dough

In the bowl of a stand mixer fitted with the dough hook, whisk together 1½ cups warm water (100–110°F) and 2¾ tsp active dry or instant yeast. Let sit for 5 minutes until bubbly.

Add in 4 cups bread flour, 1 tbsp brown sugar, and 2 tsp salt. Mix on low speed for 2 minutes until shaggy.

For protein: Replace 1 cup of bread flour with whey isolate, or blend in ½ cup Greek yogurt or cottage cheese and slightly reduce the water.

Step 2: Knead & Rise

Continue kneading on medium speed for 6–7 minutes, or by hand for 8–10 minutes on a floured surface. Dough should be soft, smooth, and slightly tacky.

Shape into a ball and place in a lightly oiled bowl. Cover and let rise at room temp for 60–90 minutes, until doubled in size.

Step 3: Shape the Bagels

Punch down the risen dough. Divide into 8 equal pieces and shape each into a ball.
Use your thumb to poke through the center, then gently stretch each one into a 1.5–2 inch ring.

Cover loosely with a towel and let them rest while preparing the water bath.

Step 4: Boil for Chew

Preheat oven to 425°F (218°C).
Bring 2 quarts water and ¼ cup honey (or barley malt syrup) to a boil. Lower heat to a gentle boil and carefully drop in 2–4 bagels at a time.

Boil each side for 1 minute. Remove with a slotted spoon and place back on the tray.

Step 5: Season & Prep to Bake

Whisk 1 egg white + 1 tbsp water for an egg wash. In a bowl, mix your everything seasoning (poppy, sesame, garlic, onion, sea salt).

Brush each boiled bagel with egg wash and dip the top into the seasoning blend. Return to parchment-lined sheet, spaced evenly.

Step 6: Bake & Cool

Bake for 20–25 minutes, rotating pans halfway through. Bagels should be deep golden brown with a crisp crust.

Let cool for 20 minutes on the pan, then transfer to a rack. Slice, toast, or freeze for later.

Pair these with a protein smoothie, eggs, protein banana muffins, or even a chocolate chip mini protein muffin for a complete high-protein breakfast that keeps you full and energized.

Nutrition Breakdown

Here’s the estimated nutrition per bagel, depending on which version you bake. Each one brings a different boost, so whether you’re going classic or packing in the protein, you’ll know what you’re getting in every bite.

📊 Classic Bagel

Calories: 260
Protein: 9g
Fat: 2.5g
Carbs: 54g

📊 With Whey Protein

Calories: 280
Protein: 16g
Fat: 2.5g
Carbs: 52g

📊 With Greek Yogurt

Calories: 290
Protein: 14g
Fat: 3g
Carbs: 50g

📊 With Cottage Cheese

Calories: 285
Protein: 13g
Fat: 3g
Carbs: 51g

Pair any of these with eggs, nut butter, or one of our chocolate chip protein muffins for a full-on breakfast that actually lasts.

Bagel Shaping, Storage & Protein-Powered Toppings That Hit

You’ve made the dough, you’ve boiled it, but how do you shape that perfect everything bagel? And what should you top it with if you’re aiming for a high protein breakfast that still tastes amazing? Don’t worry, it’s all been tested and tweaked to work, no guesswork needed.

Let’s talk form, flavor, and fuel.

Shaping Like a Pro (Without Overthinking It)

Here’s a little secret: perfectly round bagels are lovely, but rustic ones taste just as good. The key to shaping is confidence, not perfection.

Best method:
After dividing your dough into 8 pieces, shape each one into a ball, don’t stress about making them perfect. Let them chill for a few minutes so the gluten loosens up. Then, press your finger through the center and gently stretch each one into a bagel shape, about 2 inches across.

Pro tip:
If the dough pulls back or feels tight when you shape it, don’t force it. Give it a 5–10 minute breather, and it’ll be much easier to handle.

This method keeps the bagel sturdy enough to handle toppings but open enough to bake evenly with that classic ring.

How to Store Your Bagels (And Still Enjoy Them Days Later)

Homemade bagels don’t have preservatives, so freshness is key. Here’s how to keep them chewy, not stale:

Short-term:
Keep them in a tightly sealed container or zip-top bag at room temp for up to 2 days.

Midweek:
Refrigerate if needed, but toast them lightly to bring back the texture.

Freezing:
Slice them first, then wrap each half tightly in plastic or a reusable wrap. Store in a freezer bag. They’ll keep for up to 3 months. Just pop one into the toaster straight from frozen. No defrosting needed.

And yes, even the protein bagel version freezes just as well.

Best Protein Bagel Toppings: Flavor Meets Fuel

Here’s where it gets fun, and filling. If you’re building a bagel with protein as the goal, your topping choices matter. You want something that adds satiety without losing the flavor you love.

My go-to high protein toppings:

• Whipped cottage cheese + sliced tomato + black pepper
• Mashed avocado + hemp seeds + chili flakes
• Almond butter + banana slices (sweet and savory)
• Smoked salmon + light cream cheese + capers
• Hummus + egg + microgreens
• Greek yogurt + blueberries + drizzle of honey (yes, on a toasted bagel!)

Looking for flavor ideas? My bagel topping list is packed with sweet and savory inspiration. For a full meal, pair your protein everything bagel with this kale and white bean salad for lasting energy and balance.

Why This Everything Bagel Recipe Works (With or Without Protein)

You don’t need a commercial kitchen to make bakery-level bagels. This everything bagel recipe proves that flavor, flexibility, and protein can all live in one simple dough. It starts with real ingredients, nothing fancy, and ends with chewy, golden bagels you can enjoy fresh or stash for later.

Homemade Bagels > Store-Bought Every Time

Let’s be honest: store-bought bagels are convenient but often leave you feeling heavy or hungry an hour later. These homemade versions give you better texture, cleaner ingredients, and room to make it fit your needs.

Craving a high protein breakfast? Swap in a scoop of whey or stir in some blended cottage cheese. Just want a classic flavor and chew? Stick with the base. Either way, you’re getting a bagel that satisfies.

Pair them with toppings from this bagel guide or match with a protein banana muffin for serious fuel.

This Recipe Grows With You

What I love most? This recipe adapts to your season. New to baking? Skip the add-ins and just enjoy learning to shape. Need a portable protein bagel for busy mornings? Use the swaps and batch-freeze them.

Whatever version you choose, you’re not just making breakfast, you’re building a rhythm in your kitchen that works for you. And you’ll never look at store-bought bagels the same way again.

FAQs: Everything Bagel

From My Kitchen to Yours

I hope these everything bagels bring you that chewy crust, warm kitchen smell, and extra fuel your mornings deserve. Whether you go classic or protein-powered, just remember, imperfect bagels still taste amazing. (Dan once ate one I accidentally baked for 10 extra minutes… and didn’t even notice.)

f you’re still feeling inspired (or just a little hungry), here are a few more flavor-packed bakes from my kitchen to yours:

• Need a savory twist? These onion bagels bring that bold, toasty bite that tastes straight from the corner deli.

• For a high-protein treat that still feels like dessert, try my chocolate chip protein muffin, it’s Mia’s favorite after-school snack.

• And if you’re keeping things low-carb or gluten-light, these almond flour bagels deliver all the chew, none of the crash.

💬 Got a question? A bagel win (or fail) to share? Leave a comment below. I love seeing your kitchen experiments and helping them turn out even better.

And if you’re wondering who’s behind the apron and the floury counters…
Come say hi on my about page. I’m usually nearby with coffee, carbs, and a hungry teenager or two asking “are they done yet?”