This recipe for High-Protein Bagel Bites has become my go-to when I want something handheld, satisfying, and a little nostalgic without the carb overload of a full bagel. I first developed this version on a busy weekend when I had a single scoop of unflavored protein powder left in the pantry and a tub of plain Greek yogurt approaching its best-by date. The result was unexpectedly chewy, slightly tangy dough that crisps at the edges in the air fryer and hides a creamy center of cream cheese in every bite. My kids and roommates loved them as a quick snack; they disappeared faster than I could photograph them.

What makes these bites special is the texture: a soft interior with a lightly crisp exterior, rounded out by the savory crunch of Everything But The Bagel seasoning. The protein powder boosts the macronutrient profile without adding overt flavor, while gluten-free flour keeps them accessible for guests with sensitivities. I often make a double batch and freeze extras for busy mornings — they thaw and reheat beautifully. They’re ideal for lunchboxes, post-workout snacks, or when you want something that feels indulgent but is actually quite balanced.

Ingredients

• Gluten-free all-purpose flour (2/3 cup): Look for a 1:1 blend that contains xanthan gum for structure (Bob's Red Mill or King Arthur both work well). This measurement yields a tender crumb while keeping the bites light.
• Baking powder (1 teaspoon): Provides gentle lift so each bite puffs slightly in the air fryer — use aluminum-free if you prefer a cleaner taste.
• Unflavored protein powder (1 scoop, about 1 oz / 30 g): Any neutral whey or plant-based powder will work. I prefer an unflavored whey isolate for minimal impact on texture and flavor.
• Pinch of salt: Balances the dairy tang and enhances the savory seasoning on top.
• Plain unsweetened Greek yogurt (2/3 cup): Use full-fat or 2% for the creamiest texture; nonfat will work but the bites will be slightly drier. Brand-wise, Fage or Chobani give consistent results.
• Cream cheese (10 teaspoons total — about 1 teaspoon per bite): Soften slightly for easy scooping; full-fat cream cheese creates the best, creamy center.
• Egg (1, optional): Lightly beaten for an egg wash to deepen color. You can skip it and spray with neutral oil instead for a golden finish.
• Everything But The Bagel seasoning (to taste): This iconic mix (salt, sesame, poppy, garlic, onion) adds instant bagel flavor — Trader Joe's or homemade both work.
• Neutral oil spray: Optional, for crisping if you omit the egg wash.

Instructions

Combine dry ingredients: In a medium mixing bowl whisk together 2/3 cup gluten-free all-purpose flour, 1 teaspoon baking powder, 1 scoop (about 1 oz / 30 g) unflavored protein powder, and a pinch of salt until evenly distributed. Sifting is not necessary but helps avoid small clumps when using certain protein powders. Aim for a homogenous mix so each bite has the same texture. Add the yogurt and form the dough: Spoon in 2/3 cup plain unsweetened Greek yogurt and use a spatula to fold and press until a sticky dough forms. The dough should be tacky but not overly wet; if it’s too loose, add a teaspoon more flour at a time. Let it rest 1–2 minutes — the protein powder will hydrate slightly and become easier to handle. Portion and fill: Lightly flour your work surface with a dusting of gluten-free flour. Divide the dough into 10 even pieces (a small kitchen scale helps). Roll each piece into a ball, then flatten gently into a little disc. Place about 1 teaspoon of softened cream cheese in the center, fold the edges together to seal, and reshape into a smooth ball so the filling is fully enclosed. Sealing well prevents leakage during cooking. Finish and season: Place the filled balls on a parchment-lined tray. Brush each with the optional beaten egg for a glossy finish or lightly spray with oil. Generously sprinkle Everything But The Bagel seasoning on top, pressing gently so it adheres. This step is where the bagel flavor really shines. Air-fry until golden: Preheat your air fryer to 350°F (about 177°C) for 5 minutes. Arrange the bites in a single layer without overcrowding — work in two batches if necessary. Air-fry for 5–6 minutes, rotating the basket halfway if your model has hot spots, until the tops are golden and the edges have a light crust. Because models vary, check at 4 minutes on the first batch. Cool and serve: Let the bites rest 2–3 minutes before serving so the cream cheese centers set slightly. Serve warm for the best contrast between tender dough and creamy filling.

Storage Tips

Store cooled bites in an airtight container in the refrigerator for up to 4 days. For longer storage, freeze on a baking sheet until solid, then transfer to a resealable freezer bag for up to 3 months. Reheat from frozen in the air fryer at 325°F (163°C) for 6–8 minutes until warmed through, or thaw overnight in the fridge and reheat 3–4 minutes. Avoid microwaving from frozen, as the centers may heat unevenly and become overly soft.

Ingredient Substitutions

If you need dairy-free options, use a plant-based Greek-style yogurt (soy or coconut) and dairy-free cream cheese. For a lower-fat result, choose nonfat Greek yogurt, though texture will be slightly drier — add a teaspoon of olive oil if needed. Swap the unflavored protein powder for collagen peptides (not suitable for vegans) or omit entirely and add 2 tablespoons more flour; omission reduces protein density but preserves texture. If you don't have gluten-free flour, regular all-purpose flour works the same way in technique and timing.

Serving Suggestions

These bites pair beautifully with a simple side salad for a light lunch, or served alongside a bowl of soup for a cozy dinner. Garnish with a smear of flavored cream cheese, a sprinkle of fresh chives, or a dab of Dijon mustard for a savory twist. For brunch, serve with smoked salmon and capers on the side so guests can assemble open-faced mini bagels.

Cultural Background

These mini bites play on the classic flavors of the American bagel — a food with immigrant roots that became a ubiquitous breakfast staple across urban centers. Using Everything seasoning is a modern shortcut to recreate that bagel profile without boiling or baking. The adaptation into a protein-forward, bagel-inspired bite reflects contemporary trends toward portable, portion-controlled snacks that retain comforting flavors from traditional cuisine.

Seasonal Adaptations

In cooler months, add warm spices like a pinch of smoked paprika or stir in a tablespoon of finely chopped roasted shallot to the filling for depth. During summer, fold in fresh herbs — dill or chives — with the cream cheese and top with a tiny sliver of cucumber for a refreshing bite. For holiday brunches, offer a trio of fillings: herb-cream cheese, maple-candied bacon, and smoked trout mousse to showcase seasonal ingredients.

Meal Prep Tips

Prepare the dough and fill the bites ahead of time; unbaked, they keep in the fridge for up to 24 hours on a lined tray. For grab-and-go breakfasts, bake a large batch, cool, and freeze individually. Store in single-serving bags so you can reheat just what you need. Label and rotate so older portions are used first. Bring along a small insulated container to keep them warm for 1–2 hours if you’re packing them for outings.

These High-Protein Bagel Bites are small in size but big on functionality: adaptable, quick, and reliably delicious. Give them a try on a busy morning or a casual gathering — tweak the filling and seasoning to make them your own, and enjoy the convenience of a protein-focused snack that feels indulgent.