Whole Grain Protein Seed Bagels

Name: Whole Grain Protein Seed Bagels
Prep time: 30 min
Cook time: 25 min
Total time: 55 min
Yield: 8 bagels
Ingredients: 2 cups whole wheat flour; 1 cup bread flour; 1/4 cup sunflower seeds; 1/4 cup sesame seeds; 2 tablespoons chia seeds; 1 tablespoon instant yeast; 1 tablespoon honey; 1 teaspoon salt; 1 cup warm water; Cooking spray for the baking sheet

Highlighted under: Clean Healthy Food Inspiration

I absolutely love making these Whole Grain Protein Seed Bagels at home. The blend of whole grains and seeds not only enhances the bagels' texture but also boosts their nutritional value. Baking them from scratch fills my kitchen with a warm, inviting aroma, making it hard to resist sneaking one fresh out of the oven. They are versatile—perfect for breakfast or a healthy snack. Plus, the added protein means I feel satisfied longer, making these bagels a stay-on-my-counter staple for the whole family.

Created by

Nicola Fairchild

Last updated on 2026-02-16T12:29:37.353Z

Making these Whole Grain Protein Seed Bagels was a delightful adventure in my kitchen. I enjoyed experimenting with different seeds, and my favorite combination includes sesame and chia seeds for extra crunch and nutrition. The dough comes together beautifully, and kneading it by hand creates a wonderful texture that is so rewarding.

One of the best tips I can share is to let the bagels boil in a mixture of water and a touch of honey before baking. This step helps create a chewy crust that balances perfectly with the soft interior. Trust me, it makes all the difference!

Why You'll Love These Bagels
Packed with protein to keep you full and energized
A hearty yet tender texture thanks to whole grains
Versatile enough for any topping—from savory to sweet

The Importance of Whole Grains

Using whole wheat flour in these bagels not only contributes to their hearty texture but also increases their fiber content significantly. Fiber plays a crucial role in digestive health, aiding in satiety and potentially reducing cravings. This recipe combines it with bread flour, which enhances gluten structure, giving the bagels that perfect chewiness. If you're sensitive to gluten, you can substitute the whole wheat flour with a gluten-free blend, though the bagels may lose some of their characteristic texture.

Incorporating seeds like sunflower and sesame adds a nutty flavor and boosts the nutritional profile. Sunflower seeds are rich in vitamin E and magnesium, while sesame seeds provide calcium and iron. The mix of seeds not only enhances flavor but also adds necessary healthy fats, providing both richness and energy. If you want to experiment, try swapping in pumpkin seeds or flaxseeds to tailor the taste and benefits to your preference.

Perfecting Your Bagel Technique

Kneading the dough is critical to achieving the right texture. You want to knead until the dough is smooth and elastic—usually about 8-10 minutes. If the dough feels too sticky, dust in a little more flour, but be careful not to overdo it, as too much flour can make the bagels dense. A well-kneaded dough should spring back when poked, indicating the gluten has developed well.

The boiling step is essential for creating bagels that have that lovely shiny crust. Boiling them briefly helps to create a chewy exterior while keeping the inside soft. If you’re using a pot that’s too small, the bagels may not boil evenly; it’s best to work in batches so that they have enough space to float freely. Consider adding a teaspoon of baking soda to the boiling water; this can enhance the color and texture of the crust, giving them an even better finish.

Ingredients

Bagel Ingredients

2 cups whole wheat flour
1 cup bread flour
1/4 cup sunflower seeds
1/4 cup sesame seeds
2 tablespoons chia seeds
1 tablespoon instant yeast
1 tablespoon honey
1 teaspoon salt
1 cup warm water
Cooking spray for the baking sheet

Instructions

Prepare the Dough

In a large mixing bowl, combine the whole wheat flour, bread flour, sunflower seeds, sesame seeds, chia seeds, instant yeast, and salt. In another bowl, mix the warm water and honey until dissolved. Gradually add the wet ingredients to the dry ingredients and mix until a dough forms.

Knead the Dough

Turn the dough out onto a lightly floured surface and knead it for about 8-10 minutes until it is smooth and elastic. Place it in a greased bowl, cover with a damp cloth, and let it rise for 30 minutes or until doubled in size.

Shape the Bagels

Preheat your oven to 425°F (220°C) and line a baking sheet with parchment paper. Once the dough has risen, punch it down and divide it into 8 equal pieces. Shape each piece into a bagel by forming a ring and pressing a hole in the center.

Boil the Bagels

Bring a large pot of water to a boil and gently add the bagels, boiling for about 1 minute on each side. Remove them with a slotted spoon and place them on the prepared baking sheet.

Bake the Bagels

Bake the bagels in the preheated oven for about 20-25 minutes or until they are golden brown. Allow them to cool on a wire rack before serving.

Pro Tips

For added flavor, consider topping your bagels with your favorite seeds before baking. You can also experiment with different combinations like poppy seeds or even seasoning blends!

Storing and Freezing Your Bagels

Once baked, allow the bagels to cool completely on a wire rack. To store, keep them in a sealed container at room temperature for up to 3 days or in the refrigerator for up to a week. If you want to keep them longer, freezing is a great option. Simply slice the bagels before freezing; this way, you can easily toast them straight from the freezer without waiting. They will stay fresh for about 2 to 3 months in the freezer.

To reheat, pop your frozen bagel in a toaster, or for a softer option, wrap it in foil and warm it in a preheated oven at 350°F (175°C) for about 10-15 minutes. This helps retain moisture while thoroughly warming them. Enjoying them toasted with cream cheese or your choice of toppings makes for a satisfying breakfast or snack.

Serving Suggestions and Variations

These Whole Grain Protein Seed Bagels are versatile and can be topped with a variety of spreads. Cream cheese is a classic, but consider hummus, avocado mash, or nut butter for healthier options. Fresh herbs or smoked salmon can elevate them into a delightful brunch dish. For a sweet twist, smear with a combination of ricotta cheese and honey, topped with fresh fruit or berries.

You can also experiment with flavors in the bagel dough itself. Adding herbs like rosemary or thyme, or spices like cinnamon or nutmeg can give a different dimension. For a seasonal variation, try mixing in dried fruits like cranberries or apples for a deliciously unique bagel that can satisfy both sweet and savory cravings.

Questions About Recipes

→ Can I use all-purpose flour instead of whole wheat flour?

Yes, you can substitute all-purpose flour, but the bagels may be less nutritious and have a different texture.

→ How do I store leftover bagels?

Store them in an airtight container at room temperature for up to 2 days, or freeze them for longer storage.

→ Can I add flavorings to the dough?

Absolutely! You can add herbs, spices, or even shredded cheese to the dough for added flavor.

→ What’s the best way to reheat bagels?

For the best results, reheat them in the oven at 350°F (175°C) for about 5-10 minutes until warmed through.