The Complete Homemade Protein Bagels Guide – 11 Easy Recipes

A regular medium bagel contains about 50–60 grams of carbs, less than 3 grams of fiber, and only 8–10 grams of protein. In contrast, protein bagels deliver 15–25 grams of protein with fewer refined carbs and nutrient-rich ingredients like Greek yogurt, almond flour, or cottage cheese, making them a healthier, more filling upgrade that supports energy and muscle recovery.

Plain Bagel – 280–300 calories, 50–60g carbs, 8–10g protein, 2–3g fiber
Protein Bagel – 250–280 calories, 25–35g carbs, 15–25g protein, 3–5g fiber
Almond Flour Bagel – 220–250 calories, 15–20g carbs, 12–15g protein, 4–6g fiber
Greek Yogurt Bagel – 250–270 calories, 30–35g carbs, 15–20g protein, 2–4g fiber
Cottage Cheese Bagel – 240–260 calories, 25–30g carbs, 18–20g protein, 2–3g fiber

“A plain medium bagel contains about 280 calories, 50–60g carbs, and only 8–10g protein (USDA).”

Bagels are more than breakfast, they’re little circles of joy. They bring back memories of family mornings, cozy weekends, and quick bites before a busy day. At Flavors by Betty, I’ve reimagined the classic into recipes that are nourishing, balanced, and still wonderfully indulgent.

Each recipe has been tested in my kitchen until it felt just right. My goal: bagels that satisfy in the moment and fuel your body with care. This Homemade Protein bagels guide shares my favorite variations, from protein-packed to cinnamon raisin, proving that a simple bagel can fit beautifully into any lifestyle.

Table of Contents

Protein Bagels

Protein bagels are where my bagel journey truly began. After much testing, I created a recipe that delivers 15–25 grams of protein per serving, nearly double what you’d get from the bakery. Greek yogurt gives the dough structure and tenderness, while the protein boost makes each bagel filling enough to keep you energized through the morning or after a workout.

These bagels bake golden and soft, perfect for layering into a sandwich, toasting with cream cheese, or enjoying fresh from the oven. They prove that comfort food and nourishment can live happily side by side.

👉 Learn how to bake protein bagels with 15–25g of protein per serving: Protein Bagels

Everything Bagel

Few flavors feel as complete as the everything bagel. Coated in sesame seeds, poppy seeds, garlic, onion, and just the right amount of salt, it’s bold, savory, and wonderfully aromatic. What makes this bagel truly special is its versatility. It shines at breakfast with cream cheese, at brunch with smoked salmon, or at lunch layered with avocado and turkey.

For me, the everything bagel is the one I reach for when I want maximum flavor without overthinking toppings. It’s the reliable favorite that never disappoints.

👉 Master the flavor-packed everything bagel recipe with sesame, garlic, and onion topping: Everything Bagel

Best Bagel Toppings

A bagel is never just bread, it’s a foundation for endless combinations. Over the years, I’ve tested more toppings than I can count, and I’ve found that the best ones balance indulgence with nourishment.

For a protein-rich choice, avocado with a fried egg adds healthy fats and about 10–12 grams of protein. Smoked salmon with cream cheese and fresh dill is another favorite, giving a luxurious flavor boost with up to 20 grams of protein. If you’re craving something sweet, peanut butter with banana is energizing, while almond butter sprinkled with cinnamon brings warmth and coziness.

Bagels adapt beautifully to any time of day. With the right toppings, they can be breakfast, a quick lunch, a hearty afternoon snack, or even a light dinner. That’s the beauty of starting with a perfectly baked base, it’s ready to take on any story you want to tell with it.

👉 Discover the best bagel toppings for protein, sweetness, and balance: Bagel Toppings – Best Ideas

Protein Bagels with Almond Flour

The first time I swapped almond flour into a bagel recipe, I was surprised by how much character it added. Almond flour creates a naturally gluten-free bagel that’s tender, slightly nutty, and deeply satisfying. Better still, it cuts down the carbs dramatically, often 60% less than the standard recipe, while still delivering 12–15 grams of protein per serving.

These bagels are lighter on the stomach but never light on flavor. They toast beautifully, develop a golden crust, and pair well with both sweet and savory toppings. Whether you’re following a low-carb lifestyle or simply curious to try something new, almond flour bagels are a wholesome twist that doesn’t compromise on taste.

👉 Follow step-by-step almond flour protein bagel instructions for a low-carb option: Protein Bagels with Almond Flour

“Almond flour bagels average 220–250 calories and just 15–20g carbs, significantly lower than traditional flour versions USDA.”

High-Protein Bagel with Greek Yogurt

Greek yogurt has always been a secret weapon in my kitchen. It’s rich in protein, adds creaminess, and brings a natural tang that works beautifully in baked goods.

The best part is the simplicity. With just a few ingredients and no yeast required, these bagels are quick to make, perfect for mornings when time is short. They’re light, flavorful, and nourishing enough to keep you full for hours.

This is the recipe I often recommend to anyone new to baking bagels. It’s approachable, reliable, and always delivers that homemade satisfaction.

👉 Try my quick, no-yeast Greek yogurt protein bagel recipe with 20g of protein: High-Protein Bagel with Greek Yogurt

Onion Bagel

There’s something comforting about the savory sweetness of an onion bagel. As the dough bakes, caramelized onions release their aroma, filling the kitchen with warmth that feels both nostalgic and inviting.

Beyond flavor, onions bring antioxidants and a subtle depth that makes this bagel feel hearty and satisfying. It pairs beautifully with savory toppings like chive cream cheese, roasted turkey, or smoked salmon, each one highlighting the onion’s rich flavor.

For me, onion bagels are about tradition. They remind me of simple breakfasts where flavor mattered more than fuss, and they remain one of my go-to choices when I want something timeless and full of character.

👉 Bake a savory classic with this homemade onion bagel recipe: Onion Bagel

Low-Carb High-Protein Bagels

Balancing flavor with nutrition has always been at the heart of my baking, and these low-carb, high-protein bagels are one of my proudest results. While a standard bagel can carry nearly 60 grams of carbs, this version cuts that number down dramatically, sometimes by more than half, without losing the chewy bite we all love. Each one still delivers a generous 15–20 grams of protein, making it a smart option for anyone following a low-carb lifestyle or simply wanting more balanced energy.

The dough blends protein-rich ingredients with alternative flours, giving a golden, tender finish that toasts beautifully. These bagels are perfect for mornings when you need fuel that won’t cause a crash, or as a base for a hearty sandwich that feels indulgent yet fits into your goals. They remind me that healthy eating isn’t about sacrifice, it’s about clever swaps that make everyday favorites better for you.

👉 Explore a lighter take with low-carb high-protein bagel variations: Low-Carb High-Protein Bagels

Cinnamon Raisin Bagel

The cinnamon raisin bagel is the sweet spot of comfort food, literally. With warm cinnamon swirled into the dough and plump raisins dotted throughout, every bite carries the nostalgia of childhood breakfasts and cozy mornings. Unlike plain bagels, this one offers natural sweetness and a hint of spice that feels indulgent without going over the top.

Nutritionally, cinnamon brings antioxidants and warmth, while raisins provide fiber and natural energy. Toasted and topped with butter, almond butter, or even a light cream cheese, it becomes both a treat and a wholesome option. For me, the cinnamon raisin bagel is the one that makes mornings feel special, even on the busiest days.

👉 Add comfort to your mornings with this cinnamon raisin bagel recipe: Cinnamon Raisin Bagel

Are Protein Bagels Healthy?

The question I hear most often is, “Are protein bagels actually healthy?” The answer is yes, when made thoughtfully. A regular bagel tends to be carb-heavy, offering about 8–10 grams of protein against nearly 60 grams of carbs. Protein bagels, on the other hand, typically deliver 15–25 grams of protein with fewer refined carbs and more nutrient-dense ingredients.

👉 Read the full breakdown: are protein bagels actually healthy? Are Protein Bagels Healthy?

Healthiest Bagel Choices

If you’re looking for the most balanced options, here’s what I recommend based on both flavor and nutrition:

• Almond Flour Bagels – lowest in carbs, with added healthy fats and 12–15g protein.
• Greek Yogurt Bagels – quick to make, higher in protein (15–20g), and tender in texture.
• Cottage Cheese Bagels – highest protein option (~20g), light yet filling.
• Multigrain Bagels – best for fiber and sustained energy, though higher in carbs than almond flour.

👉 Takeaway: Almond flour and cottage cheese bagels are the best trade-offs if you’re prioritizing protein and fewer carbs, while multigrain bagels are ideal for long-lasting energy and fiber.

Cottage Cheese Bagels

Cottage cheese may not be the first ingredient you think of when it comes to bagels, but it’s one of my favorites to work with. Its mild flavor blends seamlessly into the dough while adding a protein boost that makes each bagel more filling. On average, these bagels deliver 15–20 grams of protein while staying tender and light.

What I love most is the texture, soft, slightly moist, and perfect for toasting. Cottage cheese brings richness without heaviness, making these bagels a wonderful option for anyone who wants a balanced breakfast that still feels indulgent. They pair beautifully with savory spreads or a drizzle of honey for a touch of sweetness.

👉 Make soft and tender cottage cheese bagels with 20g of protein: Cottage Cheese Bagels

Multigrain Bagel Recipe

The multigrain bagel is the balance-seeker’s dream. Made with a blend of flours and hearty grains like oats, flax, and sunflower seeds, it delivers more fiber, more nutrients, and a flavor that’s both earthy and satisfying. Unlike a plain bagel, which can feel heavy, this version offers texture and depth that keep each bite interesting.

Nutritionally, multigrain bagels provide sustained energy, with complex carbs that digest more slowly and help keep you full. Each serving carries protein from the added grains and seeds, making it a wholesome upgrade that feels as nourishing as it tastes. For me, these bagels are a reminder that health and heartiness can live in the same bite, simple, rustic, and endlessly versatile.

👉 Bake a hearty multigrain bagel with oats, flax, and sunflower seeds: Multigrain Bagel Recipe

Best Bagel Choices by Your Goal

Not every bagel has to serve the same purpose. Some mornings you need fuel, other days you want comfort, and sometimes you just need speed. Here’s how to choose the right one for your lifestyle:

For Weight Loss

Almond flour bagels are the lightest option, with just 15–20g of carbs compared to 50–60g in a plain bagel. The protein and healthy fats in almond flour keep you satisfied longer, helping reduce cravings. They’re perfect for anyone following a low-carb or calorie-conscious plan.

For Muscle Recovery

Cottage cheese bagels are the protein champions, offering around 18–20g per serving. That protein supports muscle repair after workouts while keeping the texture soft and tender. Pair them with smoked salmon or turkey for an even bigger recovery boost.

For Steady Energy

Multigrain bagels provide complex carbs and fiber that digest slowly, giving you fuel that lasts for hours. They’re ideal before a busy workday or an active weekend, offering both nourishment and a hearty bite. The blend of seeds and grains also adds extra nutrients.

For Speed

Greek yogurt bagels are quick and easy, no yeast, no waiting for dough to rise. Just mix, shape, and bake in under 30 minutes. Each one delivers 15–20g protein, making them the best choice when you want something warm, healthy, and fast.

👉 Think of it like this: there’s a bagel for every kind of day, and knowing which one to reach for makes life easier (and tastier).

Betty’s Expert Bagel Tips

After testing these recipes countless times in my kitchen, I’ve learned a few simple truths. Here are my favorite little tips that make a big difference:

• Don’t stress about perfect shapes, the flavor is what counts.
• Let the dough rest for 10 minutes before shaping if you want extra chewiness.
• Brush with egg wash for that golden bakery-style finish.
• Toast before topping, it brings out the nutty notes in almond flour and the sweetness of raisins.
• Freeze extras so you always have a healthy bagel ready to go.

👉 Imperfection is part of the story. A lopsided bagel is still a beautiful one, especially when it’s made with love.

FAQ – Homemade Protein Bagels

Let’s Keep Baking Together

Bagels aren’t about perfection, they’re about joy. Some of mine come out perfectly round, others a little lopsided, but every one is baked with love. That’s what I want you to feel when you try these recipes in your own kitchen.

Don’t wait until you “get it right”, just start. Try the almond flour version, whip up the Greek yogurt bagel, or roll a cinnamon raisin on a cozy morning. Each bake is a little experiment, a little act of love, and always worth it.

I’d love to hear how yours turn out. Leave me a comment, share your favorite topping, or tell me which recipe made your family smile. After all, food is better when it’s shared, stories and all.

With love (and a touch of flour on my apron),
Betty 💛

👉 Keep exploring more of my recipes here: Flavors by Betty – Recipes
👉 Curious about my kitchen journey? Visit my About Me page.