Whole Grain Protein Seed Bagels

Name: Whole Grain Protein Seed Bagels
Prep time: 30 min
Cook time: 25 min
Total time: 55 min
Yield: 12 bagels
Ingredients: 3 ½ cups whole grain flour; ½ cup vital wheat gluten; 1 tablespoon instant yeast; 1 tablespoon honey or maple syrup; 1 tablespoon salt; 1 ½ cups warm water; ½ cup mixed seeds (sesame, poppy, flax, sunflower); 1 tablespoon olive oil for greasing

Highlighted under: Clean Inspiration

I love making these Whole Grain Protein Seed Bagels because they’re not just a delicious breakfast option; they're packed with nutrients that keep me energized throughout the day. Each bite is a satisfying blend of whole grains and seeds that adds a lovely crunch. The process is surprisingly simple, and I find that making bagels at home is a fulfilling experience. These bagels also freeze beautifully, making them perfect for quick meals any time of the week.

Created by

Tamsyn Calder

Last updated on 2026-02-16T12:21:37.178Z

When I first decided to make my own bagels, I knew I wanted something wholesome and flavorful. These Whole Grain Protein Seed Bagels turned out to be the perfect merge of health and taste. Each ingredient serves a purpose, enhancing not just the flavor, but also the nutritional profile of each bagel.

I experimented with various toppings and found that a sprinkle of everything bagel seasoning adds incredible flavor without overpowering the whole grain base. Baking them at a high temperature gives a beautifully chewy texture, while still keeping them light enough to enjoy at any time.

Why You Will Love These Bagels
Nutrient-dense with a delightful crunch from mixed seeds
Easy to customize with your favorite toppings
Homemade freshness that beats any store-bought bagel

Understanding Whole Grain Flour

Whole grain flour is a crucial ingredient in these bagels, adding not only a hearty flavor but also significant nutritional benefits. It retains the bran and germ of the grain, which contributes fiber and essential vitamins. This results in a denser bagel compared to those made with all-purpose flour. If you can't find whole grain flour, you can use a mixture of whole wheat flour and all-purpose flour, but be aware that the texture and flavor profile will change.

The hydration level in whole grain flour is different from white flour, often requiring slightly more water. Therefore, keep an eye on the dough consistency as you mix. If the dough seems too dry, adding an extra tablespoon or two of warm water can help achieve the right elastic texture, crucial for the bagel's chewiness.

Mastering the Boiling Step

Boiling bagels before baking is what gives them their signature chewy crust. When you place the bagels in boiling water, it creates a gelatinized layer of starch on the outside, helping to retain moisture during baking. It's important to use a large pot so the bagels have enough room to float and cook evenly. If you find the bagels are sinking rather than floating, this can indicate that they may be slightly under-proofed; try letting them rise a bit longer next time.

Timing is also critical when boiling the bagels. A 1-2 minute boil on each side ensures the bagels are cooked properly without becoming too tough. If you prefer an even chewier exterior, you can increase the boiling time by 30 seconds. Just keep a close eye to ensure they don’t become too soft before baking.

Storage and Freezing Tips

These bagels freeze wonderfully, making them a great option for meal prep. Once fully cooled, wrap each bagel tightly in plastic wrap and then place them in an airtight container or a freezer bag. This can help prevent freezer burn and preserve their flavor for up to three months. When you're ready to enjoy one, simply pop it in the toaster or let it thaw at room temperature for a quick breakfast treat.

For optimal texture after freezing, consider reheating the bagels in an oven preheated to 375°F (190°C) for about 10-15 minutes. This will help restore their fresh-baked taste and chewy texture. If you prefer a softer bagel, microwaving for 20-30 seconds can also work, but avoid overdoing it, as this can lead to a gummy consistency.

Ingredients

For the Bagels

3 ½ cups whole grain flour
½ cup vital wheat gluten
1 tablespoon instant yeast
1 tablespoon honey or maple syrup
1 tablespoon salt
1 ½ cups warm water
½ cup mixed seeds (sesame, poppy, flax, sunflower)
1 tablespoon olive oil for greasing

Preparation

Instructions

Prepare the Dough

In a large mixing bowl, combine the whole grain flour, vital wheat gluten, and salt. In a separate bowl, dissolve the honey in warm water and add the yeast, letting it sit for about 5 minutes until foamy. Gradually add the wet ingredients to the dry, mixing until a dough forms.

Knead the Dough

Turn the dough onto a floured surface and knead for about 10 minutes until smooth and elastic. You can add a bit more flour if the dough is too sticky. After kneading, place it in a greased bowl, cover it, and let it rise until doubled, about 1 hour.

Shape the Bagels

Once the dough has risen, punch it down and divide it into 12 equal pieces. Roll each piece into a ball, then poke a hole in the center with your fingers and stretch it to form a bagel shape. Place them on a baking sheet lined with parchment paper.

Boil the Bagels

Preheat your oven to 425°F (220°C). In a large pot of boiling water, add the bagels a few at a time and boil for about 1-2 minutes on each side. Remove and place back on the baking sheet.

Add Toppings and Bake

Before baking, brush the top of each bagel with water and sprinkle with the mixed seeds. Bake for 20-25 minutes until golden brown.

Cool and Enjoy

Remove the bagels from the oven and let them cool on a wire rack. Enjoy fresh or store them in an airtight container.

Enjoy Your Bagels

Pro Tips

For an extra flavor boost, try adding dried onion or garlic to the seed mix. These add-ins create an incredibly aromatic smell while baking and a savory punch to each bite.

Flavor Variations

Feel free to customize the flavor of your bagels by adding various seeds or herbs directly into the dough before kneading. Ingredients like garlic powder, onion powder, or even dried herbs like rosemary can elevate the taste profile significantly. Experimenting with different seed combinations can also result in unique flavors. I enjoy adding caraway seeds for an earthy twist—perfect for pairing with cream cheese.

Another great variation is to incorporate sweet elements such as cinnamon and raisins for a breakfast twist, or even a touch of cocoa powder for a chocolatey treat. Remember that adjusting moisture levels might be necessary with these additions, so keep an eye on the dough consistency.

Serving Suggestions

These whole grain bagels make a fantastic base for a variety of toppings. Classic cream cheese is always a winner, but consider trying avocado mash with red pepper flakes for a nutritious, trendy option. Additionally, smoked salmon paired with capers and cream cheese creates a gourmet brunch experience that's hard to beat.

For sweeter options, slathering peanut butter or almond butter, topped with bananas or berries, can turn your bagels into a fulfilling snack or breakfast. The nutty flavors of the whole grains pair beautifully with these toppings, creating not only a delicious but also a wholesome meal.

Questions About Recipes

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

Yes, but the texture and flavor will differ. Whole grain flour gives a nuttier taste and denser texture.

→ How do I store leftover bagels?

Store them in an airtight container at room temperature for up to 3 days, or freeze them for up to 3 months.

→ Can I customize the seed mix?

Absolutely! Feel free to experiment with your favorite seeds or add herbs for unique flavors.

→ What’s the purpose of vital wheat gluten?

Vital wheat gluten helps give the bagels their chewy texture. It's particularly helpful when using whole grain flour.