Bagels have long been a beloved breakfast staple, but traditional versions can be high in refined carbohydrates and lack protein. If you’re looking for a nutritious alternative that still delivers on taste and texture, homemade protein bagels are the perfect solution.
These bagels are soft, fluffy, and packed with over 13 grams of protein each—making them a fantastic option for breakfast, meal prep, or even a post-workout snack.
The best part? You only need two main ingredients: flour and Greek yogurt. No yeast, no complicated rising times, and no unnecessary additives. With just a few simple steps, you can enjoy fresh, high-protein bagels in under 30 minutes.
Whether you’re a fitness enthusiast, someone following a high-protein diet, or simply love baking healthier alternatives, these bagels are sure to become a go-to recipe.

Why Make Protein Bagels at Home?
- Quick & Easy: Traditional bagel recipes often require yeast, long resting times, and complex techniques. This version eliminates all of that, allowing you to whip up fresh bagels in no time.
- Nutrient-Dense & High-Protein: Unlike store-bought bagels, which can be high in sugar and preservatives, these bagels are made with Greek yogurt, providing a rich source of protein, calcium, and probiotics.
- Soft & Delicious: Despite their simple ingredients, these bagels don’t sacrifice taste or texture. They’re soft, chewy, and can be customized with your favorite toppings.
- Versatile: Enjoy them plain, top them with seeds, or stuff them with savory or sweet fillings. Whether it’s avocado and eggs for breakfast or smoked salmon for lunch, the possibilities are endless.
- Meal Prep Friendly: Make a batch ahead of time and store them for easy grab-and-go meals throughout the week.
Ingredients & Substitutes
This recipe uses only a handful of simple ingredients, making it accessible for everyone. Here’s what you need and potential substitutions:
- Flour: All-purpose flour is ideal for a soft and fluffy texture. If you prefer a whole wheat version, keep in mind that the bagels will be denser. For a low-carb option, substitute with almond flour, but you may need to adjust the liquid ratio.
- Greek Yogurt: Full-fat Greek yogurt (5% or 2% fat) is best for a rich taste and softer dough. You can use non-fat yogurt, but the texture may be slightly firmer. Lactose-free yogurt also works as a great alternative.
- Baking Powder: This acts as the leavening agent, helping the bagels rise without yeast. If using self-rising flour, you can omit this ingredient.
- Salt: Kosher salt or sea salt enhances the flavor of the dough.
- Egg or Egg White (Optional): Brushing the bagels with an egg wash before baking creates a beautiful golden crust.
- Toppings: Customize your bagels with sesame seeds, poppy seeds, everything bagel seasoning, sunflower seeds, or even a sprinkle of cheese for extra flavor.
How to Make Protein Bagels from Scratch
Step 1: Make the Dough
- In a large mixing bowl, combine the all-purpose flour, baking powder, and salt.
- Add the Greek yogurt and mix until the dough starts to form. If the mixture is too sticky, add a little more flour. If too dry, add a small amount of yogurt.
Step 2: Shape the Bagels

- Transfer the dough to a floured surface and knead gently until smooth.
- Divide the dough into four equal portions.
- Roll each portion into a log, about 6 inches long, and form a ring shape by connecting the ends.
Step 3: Add Toppings & Bake
- Preheat your oven to 375°F (190°C) or preheat your air fryer to 280°F (140°C).
- Place the shaped bagels on a parchment-lined baking sheet.
- If using, brush the tops with an egg wash and sprinkle your desired toppings.
- Baking:
- Oven Method: Bake for 20-25 minutes until golden brown. Let cool for at least 15 minutes before serving.
- Air Fryer Method: Air fry at 280°F (140°C) for 15-20 minutes until golden brown. Let cool before serving.
Pro Tips for Perfect Protein Bagels
- Use Full-Fat Greek Yogurt: This improves the texture, making your bagels softer and richer in flavor.
- Don’t Over-Knead the Dough: Overworking the dough can make the bagels tough rather than light and chewy.
- Monitor Baking Time: Keep an eye on your bagels to ensure they don’t become too dry or overcooked.
- Allow to Cool: Let the bagels cool for at least 15 minutes before slicing to get the best texture.

Nutritional Information (Per Bagel)
- Calories: 218 kcal
- Protein: 13.7g
- Carbohydrates: 37.3g
- Fat: 1.7g
- Fiber: 1.4g
- Sugar: 1.8g
(Note: Nutrition values may vary based on specific ingredients used.)
Storage Tips
- Room Temperature: Store in an airtight container for up to 2 days.
- Refrigeration: Keep in the fridge for up to 4 days.
- Freezing: Freeze in a sealed bag for up to 3 months. Thaw at room temperature or reheat in a toaster oven.
Serving Suggestions
These protein bagels are incredibly versatile and can be paired with a variety of toppings and fillings. Here are some ideas:
Savory Options:
- Scrambled eggs and avocado
- Smoked salmon with cream cheese and capers
- Turkey, cheese, and spinach
- Hummus with cucumber and tomato
Sweet Options:
- Peanut butter and banana
- Greek yogurt with honey and berries
- Almond butter with cinnamon and apples
Final Thoughts
Making homemade protein bagels is an excellent way to enjoy a classic breakfast favorite while keeping your diet balanced and nutritious.
With just a few simple ingredients, you can create a high-protein, delicious alternative to traditional bagels. Whether you enjoy them fresh, toasted, or packed for a meal on the go, these bagels will keep you satisfied and fueled throughout the day.
Give this easy recipe a try and discover just how simple and delicious homemade protein bagels can be!
