High Protein Bagel Bites

Featured in Elegant Small Bites.

These gluten-free bagel bites combine protein powder and creamy cream cheese for a satisfying bite. Using gluten-free flour and Greek yogurt creates a tender dough that’s easy to handle. Each bite is filled with a smooth cheese center, sealed tight and brushed with an egg wash or oil before seasoning. Cooking them in the air fryer results in a golden, slightly crisp exterior with a soft interior. They’re perfect for a quick breakfast or snack and keep well stored for several days.

Ideal for a gluten-free diet, these bagel bites offer a protein boost while delivering familiar savory flavors and a pleasant texture. The Everything But The Bagel seasoning adds a flavorful touch without overpowering the mild dough and creamy center. Easy to prepare and quick to cook, they make great options for meal prep or lunch boxes.

Barbara Chef
Updated on Sun, 25 Jan 2026 17:38:43 GMT
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A wooden cutting board with a bowl of food on it. | gracefulflavors.com

These high-protein bagel bites are a fantastic gluten-free option that comes together quickly in the air fryer. Soft on the inside with a creamy cream cheese center, they’re perfect for busy mornings or a satisfying snack anytime you need a boost.

I first made these when I wanted something easy and filling before work. Now they’re a regular in my weekend breakfast routine, especially when I need a snack that won’t weigh me down.

Ingredients

  • Gluten-free all-purpose flour: the base that keeps these bites tender; choose a blend with xanthan gum for best texture
  • Baking powder: helps the bagel bites rise and stay light
  • Unflavored protein powder: boosts protein content without altering taste; use a neutral whey or plant-based powder
  • Pinch of salt: enhances all the flavors
  • Plain unsweetened Greek yogurt: adds moisture and tang while keeping it healthy; full fat works best for richness
  • Cream cheese: the creamy surprise inside each bite; use softened for easy spreading
  • Egg, lightly beaten: optional for brushing, helps achieve a nice golden finish
  • Everything But The Bagel seasoning: adds a savory, crunchy topping that makes these feel special

Step-by-Step Instructions

Mix the Dry Ingredients:
In a mixing bowl, combine gluten-free flour with baking powder, protein powder, and salt. Mixing these well ensures an even rise and balanced flavor throughout your dough.
Add the Greek Yogurt:
Stir in the plain Greek yogurt until a sticky dough forms. The yogurt gives both moisture and a tender crumb so the bagel bites are soft but sturdy.
Shape the Dough:
Lightly flour your work surface and divide the dough into ten equal pieces. Roll each piece into a small ball, then flatten it gently in your palm.
Fill with Cream Cheese:
Place about one teaspoon of softened cream cheese in the center of each flattened dough piece. This creamy filling will melt as they cook, creating a delightful surprise.
Seal and Reshape:
Carefully pinch the dough around the cream cheese to seal it, then roll gently to reshape into a smooth ball, ensuring no filling escapes during cooking.
Add Finishing Touches:
Brush the bagel bites with beaten egg for a golden crust or use cooking spray if you prefer. Sprinkle each with Everything But The Bagel seasoning to give them that classic bagel flavor.
Preheat the Air Fryer:
Set your air fryer to 350 degrees Fahrenheit and let it heat up for five minutes. Preheating is key for achieving a crispy outside while keeping the inside tender.
Cook Until Golden:
Place the bagel bites in the air fryer basket and cook for five to six minutes. They should turn a warm golden brown on top when they are done.
Let Them Cool Slightly:
Remove the bagel bites and allow them to cool for a couple of minutes. This step helps the cream cheese set a little for easier handling and better flavor.
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A plate of food with a bowl of soup. | gracefulflavors.com

My favorite part has to be the creamy center. One weekend afternoon, I made these for a family brunch and everyone ended up reaching for seconds. The contrast between the soft dough and tangy cream cheese always brings a smile.

Storage Tips

Store leftovers in an airtight container at room temperature for up to four days. Reheat in the air fryer for a few minutes to bring back that fresh-baked crispness. You can also freeze the bagel bites individually and air fry from frozen for about five minutes before enjoying.

Ingredient Substitutions

If you don’t have protein powder, you can leave it out but expect a softer texture and less protein. Use flavored Greek yogurt like honey or vanilla for a subtle twist on flavor but reduce any sweet toppings to balance. In place of the Everything But The Bagel seasoning, you can use sesame seeds, poppy seeds, or your favorite herb blend.

Serving Suggestions

These bagel bites are delicious on their own but try pairing them with a fresh fruit salad or your favorite smoothie for a complete breakfast. They work well as a protein-packed snack during the day or tucked inside a lunchbox with some fresh veggies.

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A wooden tray with 6 balls of food on it. | gracefulflavors.com

Frequently Asked Questions

→ Can I make these bagel bites without protein powder?

Yes, you can omit the protein powder and slightly increase the gluten-free flour to maintain dough consistency. This will keep the texture similar but with a bit less protein.

→ What’s the purpose of the Greek yogurt in the dough?

Greek yogurt adds moisture and tenderness to the dough while contributing to a slight tang that balances the creamy filling well.

→ Can I bake the bagel bites instead of air frying?

Absolutely. Bake at 350°F for about 12-15 minutes or until golden brown. Keep an eye to avoid overcooking.

→ How should I store leftover bagel bites?

Store them in an airtight container in the refrigerator for up to 4 days. They can also be frozen and reheated in the air fryer.

→ What are some alternative seasonings to Everything But The Bagel?

Try garlic powder, smoked paprika, or Italian herbs for different flavor profiles that complement the creamy cheese filling.

Gluten-Free High Protein Bites

Gluten-free bagel bites filled with cream cheese, perfect for quick breakfasts or snacks, air fryer cooked.

Prep Time
10 Minutes
Cook Time
6 Minutes
Total Time
16 Minutes
By: Barbara

Category: Tasty Snacks

Difficulty: Easy

Cuisine: American

Yield: 10 Servings (10 bagel bites)

Dietary: Vegetarian, Gluten-Free

Ingredients

→ Dry Ingredients

01 ⅔ cup all-purpose gluten-free flour
02 1 teaspoon baking powder
03 1 scoop (30 g) unflavored protein powder
04 Pinch of salt

→ Wet Ingredients

05 ⅔ cup plain unsweetened Greek yogurt
06 1 egg, lightly beaten (optional, for egg wash)

→ Fillings and Seasonings

07 10 teaspoons cream cheese (approximately 1 teaspoon per bite)
08 "Everything But The Bagel" seasoning, to taste

Instructions

Step 01

In a mixing bowl, combine gluten-free flour, baking powder, protein powder, and salt until evenly incorporated.

Step 02

Stir in Greek yogurt and mix thoroughly to create a sticky dough.

Step 03

Lightly flour the work surface, then divide dough into 10 equal portions. Roll each portion into a ball.

Step 04

Flatten each dough ball and place 1 teaspoon of cream cheese in the center. Seal the dough around the filling and reshape into a smooth ball.

Step 05

Brush each ball with egg wash or lightly spray with oil. Evenly sprinkle "Everything But The Bagel" seasoning over the tops.

Step 06

Preheat the air fryer to 175°C (350°F) for 5 minutes.

Step 07

Place bagel bites in the air fryer basket without overcrowding. Cook at 175°C (350°F) for 5 to 6 minutes or until golden brown.

Step 08

Allow bagel bites to cool slightly before serving warm.

Notes

  1. Store in an airtight container for up to 4 days. For longer storage, freeze and reheat at 175°C (350°F) in the air fryer for 4 to 5 minutes. Ideal for meal prep and lunch boxes.

Tools You'll Need

  • Air fryer
  • Mixing bowl
  • Measuring cups and spoons
  • Pastry brush (optional)

Allergy Information

Please check ingredients for potential allergens and consult a health professional if in doubt.
  • Contains dairy and egg (optional)

Nutrition Facts (Per Serving)

It is important to consider this information as approximate and not to use it as definitive health advice.
  • Calories: 95
  • Total Fat: 3 g
  • Total Carbohydrate: 7 g
  • Protein: 8 g