These Protein Bagels With Almond Flour Are So Good, Even the Kids Ate Them

These almond flour protein bagels are chewy, nutty, and naturally high in protein from Greek yogurt, egg, and almond flour. With just 6g protein per bagel, they’re perfect for a quick 30-minute breakfast or post-workout snack, no yeast, no fuss.

Okay, confession time, my first batch of almond flour bagels came out so dense that Mia tapped one on the counter and said, “Mom, these are bagel rocks.” But after a few tweaks (and plenty of taste-testing around our Jersey City kitchen table), I finally found the balance.

These protein bagels are soft on the inside, golden on the outside, and strong enough to hold cream cheese, eggs, or even a full sandwich. They’re gluten-free, lower in carbs than the usual bagel shop version, and they’ll keep you full way longer.

If you’re serious about upping your breakfast game, don’t miss my Low Carb High Protein Bagels, another family favorite.

Almond Flour Protein Bagels (Keto-Friendly & Gluten-Free)

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• Author: Betty Thompson
• Total Time: 30 minutes
• Yield: 6 bagels 1x
• Diet: Gluten Free

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Description

These almond flour protein bagels are soft, chewy, and ready in just 30 minutes — made with almond flour, Greek yogurt, and an egg. Topped with everything bagel seasoning, they’re high in protein, low in carbs, and naturally gluten-free. A perfect keto-friendly breakfast or snack!

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Ingredients

Scale 1x2x3x

• 1 cup almond flour

• 1 tsp baking powder

• 1/4 tsp salt

• 1/2 cup Greek yogurt

• 1 large egg

• Everything bagel seasoning (to taste)

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Instructions

• Preheat oven to 350°F (175°C) and line a baking sheet with parchment paper.

• Mix Dry Ingredients in a bowl: almond flour, baking powder, and salt.

• Add Wet Ingredients: Add Greek yogurt and egg. Mix well until a dough forms.

• Shape Bagels: Divide into 6 portions, roll into logs, and shape into rings.

• Top with Seasoning: Place on the baking tray and sprinkle with everything seasoning.

• Bake for 20–22 minutes or until golden brown.

• Cool on a wire rack before serving.

Notes

1. Dough Handling Tip:
   If the dough feels too sticky to shape, dust your hands with almond flour or chill it in the fridge for 5–10 minutes.

2. Seasoning Swap:
   Don’t love everything seasoning? Try sesame seeds, poppy seeds, or leave them plain for a sandwich-ready bagel base.

3. Make-Ahead Friendly:
   These bagels store well in the fridge for up to 5 days or freeze beautifully for up to 2 months. Reheat in a toaster for best texture.

4. Dairy-Free Option:
   Substitute Greek yogurt with a thick, unsweetened dairy-free alternative like coconut yogurt to make it dairy-free and paleo-friendly.

• Prep Time: 10 minutes
• Cook Time: 20 minutes
• Category: Breakfast, Snack, Lunch
• Cuisine: American

Nutrition

• Serving Size: 1 bagel
• Calories: 145
• Sugar: 1g
• Sodium: 210mg
• Fat: 11g
• Saturated Fat: 1,5g
• Carbohydrates: 5g
• Fiber: 2g
• Protein: 6g
• Cholesterol: 35mg

Ingredients for Protein Bagels with Almond Flour

Core Ingredients

• 2 cups almond flour – use finely blanched for the smoothest texture. Almond meal will make bagels crumbly.
• 1 tbsp baking powder – freshness matters so the bagels rise properly.
• ½ tsp salt – balances the nutty flavor of almond flour.
• 1 cup plain Greek yogurt (nonfat or 2%) – the key protein booster. Strain if watery.
• 1 large egg – helps everything bind together. Room temperature works best.
• 2 tbsp everything bagel seasoning – optional but makes them taste bakery-style.

Why Almond Flour Works

Almond flour gives these bagels a naturally gluten free texture and a gentle nutty taste. It also lowers carbs compared to regular flour.

How to Make Protein Bagels with Almond Flour

Step-by-Step Directions

Step 1: Mix your base.
In a medium bowl, whisk together 2 cups almond flour, 1 tbsp baking powder, and ½ tsp salt. This step is like setting the stage. Almond flour brings the nutty richness, while baking powder makes sure your bagels don’t come out flat like pancakes.

Step 2: Add the protein power.
Spoon in 1 cup plain Greek yogurt and crack in 1 large egg. Mix with a sturdy spoon until it forms a dough. At first, it might look crumbly. Keep stirring. The protein from the yogurt and egg binds the almond flour into something that actually looks like bread dough.

Step 3: Shape your bagels.
Divide the dough into 6 equal pieces. Roll each piece into a ball, then poke a hole through the center with your thumb. Gently stretch the hole until it’s about 1½ inches wide. Remember, the hole will shrink as they bake. Mine used to close up completely until I learned this trick.

Step 4: Add toppings.
Place your bagels on a parchment-lined baking sheet. Brush the tops lightly with water or beaten egg, then sprinkle with everything bagel seasoning (or sesame seeds, cinnamon, or whatever you love). This little step makes them taste like they came straight from a bakery.

Step 5: Bake to golden perfection.
Bake at 375°F (190°C) for 20–22 minutes until golden brown on top and firm to the touch. Let them cool for at least 10 minutes before slicing. I know it’s hard to wait, but cooling lets the proteins set so the bagel doesn’t fall apart in your hands.

Betty’s First Failures

I’ll be honest, my first try ended with bagels that looked more like sad cookies. Jordan called them “bagookies.” The secret I learned is balancing almond flour with just the right amount of Greek yogurt. Too little and you get dry bricks, too much and the dough oozes like paste.

Tips for Perfect Texture

• Chill the dough for 10 minutes if it feels sticky.
• Use finely blanched almond flour, not almond meal.
• Don’t skip the egg wash or water brush. It helps seasoning stick.
• Rotate your baking sheet halfway for even browning.

For another fun variation, you’ll love my Cinnamon Raisin Bagel.

Nutrition & Benefits

Nutrition Facts per Bagel

Here’s the breakdown for 1 protein bagel with almond flour (out of 6 bagels, using Greek yogurt and egg):

• Calories: ~210
• Protein: 10 g
• Carbs: 9 g
• Fiber: 3 g
• Fat: 15 g
• Sugar: 2 g
• Net Carbs: 6 g

(Values may vary slightly based on the yogurt and flour you use.)

Why Protein Bagels Are a Smart Swap

Traditional bagels are famous for being carb bomb, some pack 50 grams of carbs and less than 8 grams of protein per serving. These almond flour bagels flip that script. By blending almond flour, Greek yogurt, and egg, you get:

• Double the protein compared to a classic white bagel.
• Far fewer carbs, which keeps your energy steady instead of crashing.
• Healthy fats from almonds that help you stay full longer.

Comparing to Regular Bagels

Let’s put it side by side:

These numbers show why almond flour bagels are a favorite for folks who want a high-protein, low-carb lifestyle without giving up their morning bagel.

Extra Benefits

• Gluten free and naturally grain free.
• Meal prep friendly since they store and freeze well.
• Versatile base for both sweet and savory toppings.
• Family-approved. Even Dan, who is usually “Team New York Bagel,” admits these are surprisingly good.

If you’re curious about the bigger picture, I break it all down in Are Protein Bagels Healthy?.

Variations & Substitutions

Dairy-Free or Vegan Swaps

Not a fan of Greek yogurt or eggs? You can still make these almond flour bagels.

• Yogurt Swap: Use coconut yogurt for a dairy-free option. It adds creaminess without dairy.
• Egg Swap: Mix 1 tbsp ground flaxseed with 3 tbsp water, let sit 5 minutes, and you’ve got a flax “egg.”
• Pro Tip: Vegan versions may be a touch softer, but toasting them helps firm up the bite.

Low-Carb & Keto Adjustments

Already these bagels are lower in carbs than traditional bagels, but here’s how to make them even more keto-friendly:

• Replace some almond flour with 1 tbsp psyllium husk powder for more fiber and structure.
• Reduce baking powder slightly if you’re sensitive to sodium.
• Stick with full-fat Greek yogurt or coconut yogurt to keep the fat macros keto-approved.

Fun Flavor Twists

Think beyond plain. With a few tweaks, you can make a whole bakery lineup at home:

• Everything Protein Bagels – the classic. A crunchy, salty, garlicky topping that goes with everything.
• Cinnamon Protein Bagels – add 1 tsp cinnamon and 1 tbsp honey or monk fruit sweetener into the dough. Perfect with almond butter.
• Cheesy Protein Bagels – sprinkle shredded cheddar or parmesan on top before baking. Melty goodness in every bite.
• Sweet Berry Bagels – fold in a handful of freeze-dried blueberries or raspberries before shaping.

Betty’s Kitchen Note

Don’t be afraid to experiment. My son Jordan once asked for “pizza bagels,” so I topped them with marinara and mozzarella right after baking. He said it was the best after-school snack he’s ever had.

If you like flavor twists, don’t miss my Multigrain Bagel Recipe for another hearty, family-approved bagel.

Storage, Freezing & Meal Prep

Storing Fresh Bagels

Keep your almond flour protein bagels fresh for up to 3 days at room temperature. Store them in an airtight container lined with parchment paper to prevent sticking. If your kitchen runs hot (hello, Jersey City summers), refrigerate them instead to keep them from getting too soft.

Freezer-Friendly Tips

These bagels freeze like champs. Here’s how to do it right:

1. Let them cool completely. Freezing warm bagels traps steam and makes them soggy later.
2. Slice before freezing. That way, you can pop halves straight into the toaster.
3. Wrap each bagel in parchment, then tuck into a freezer bag. Squeeze out excess air.
   They’ll stay good for up to 2 months.

Jordan once tried sneaking one straight from the freezer, thinking it was an ice bagel. He spit it out immediately. Don’t do what he did.

Meal Prep Breakfast Ideas

These bagels are a lifesaver when mornings get hectic. Try:

• Egg & Avocado Bagel Sandwich: Pile scrambled eggs, sliced avocado, and hot sauce on a toasted bagel.
• Protein Bagel Pizza: Toast and top with marinara, mozzarella, and turkey pepperoni. Great after workouts.
• Sweet Start: Spread almond butter and add sliced bananas for a quick on-the-go breakfast.

Internal link: For more protein-packed breakfast inspo, check out my 6 High Protein Bagel Recipes.

Best Toppings & Serving Ideas

Savory Toppings

These almond flour bagels hold up beautifully under hearty toppings. Some favorites around my table:

• Smoked salmon with cream cheese and capers – the classic “lox bagel” but lighter thanks to fewer carbs.
• Avocado smash with poached egg – rich, creamy, and loaded with healthy fats.
• Turkey and spinach with mustard – a protein-stacked lunch that won’t leave you sleepy.
• Hummus with roasted veggies – a dairy-free option that still feels satisfying.

Sweet Toppings

Sometimes you just want a little sweetness. These protein bagels are perfect for that too:

• Almond butter with sliced bananas – Jordan’s favorite pre-soccer snack.
• Whipped cream cheese with blueberries – Mia calls this “bagel cheesecake.”
• Cinnamon butter with apple slices – cozy fall vibes in every bite.
• Greek yogurt drizzle with honey and walnuts – turns breakfast into dessert.

Bagel Sandwich Ideas

Bagels are made for stacking. Here are combos that work any time of day:

• Breakfast Bagel: Scrambled eggs, turkey bacon, and cheddar on a toasted bagel.
• Post-Workout Fuel: Grilled chicken, avocado, and a little hot sauce.
• Quick Lunch: Tuna salad with celery and lettuce for crunch.
• Family Favorite: Peanut butter and jelly (yes, even on protein bagels).

Betty’s Family Pick

Dan swears by the smoked salmon bagel, but Mia insists the almond butter and banana combo wins. I just smile because either way, they’re eating a protein-packed breakfast and not asking me for cereal an hour later.

Troubleshooting & Common Mistakes

Why Bagels Turn Out Dense

Almond flour doesn’t behave like regular flour. If your bagels feel heavy or gummy, it’s usually because you added too much flour or didn’t whisk the dry ingredients well. Mix gently, and don’t pack the flour into the cup.

How to Fix Dry Texture

Dry bagels usually mean too little yogurt or baking too long. Add a spoonful of extra Greek yogurt if the dough looks crumbly. Watch your oven closely since almond flour browns faster than wheat flour.

Avoiding Flat or Spreading Bagels

Bagels spreading into pancake shapes is almost always from over-wet dough. If this happens, stir in another tablespoon of almond flour. Also, shape the bagels with a firm hand and stretch the hole wider than you think you need.

Family Kitchen Fail

One morning, I rushed and forgot the baking powder. The result? Almond flour hockey pucks. Jordan laughed so hard he asked if he could use one as a frisbee. Lesson learned: double-check your ingredients before mixing.

Quick Fix Tips

• Chill sticky dough for 10 minutes before shaping.
• Always use parchment paper to avoid sticking disasters.
• Rotate the baking sheet halfway through for even browning.
• Don’t slice bagels hot from the oven. Cooling lets them firm up.

If you want more guidance on baking basics, my Protein Bagels recipe has extra troubleshooting notes.

Your Questions Answered

That’s the Last Bite (and Maybe the First of Your New Bagel Routine)

If your kitchen smells like toasted almonds and fresh-baked bread right now, congrats, you just made bagels that taste like they belong in a bakery window. And you did it without a single plastic-wrapped sleeve.

Here’s what to check out next if you’re still in a bagel mood (or just hungry):

👉 More From Betty’s Kitchen (Protein-Packed Picks)

• Craving even more variety? My Everything Bagel is crunchy, garlicky, and a family favorite.
• Need grab-and-go breakfast? These Blueberry Protein Muffins hit the sweet spot without the sugar crash.
• Planning a brunch spread? Pair these bagels with my Cottage Cheese Bagels for a fun side-by-side taste test.

💬 Your Turn at the Table
Did your dough behave or did it fight back like mine did the first time? Leave a comment with your wins, your fails, or even your topping masterpieces. My crew, Mia, Jordan, Dan, and our very sneaky dog, always vote on what makes it to the blog next.

📸 Bake It, Save It, Share It
Hit the “Pin” button to save this protein bagel recipe for later. And if you bake them, tag @flavorsbybetty so I can cheer you on (yes, even if your bagels look a little… artistic). We’ve all been there.

🕒 Last Updated: September 2025

Written by Betty, Jersey-raised, protein-obsessed, and still testing recipes in a real kitchen with real critics.