Healthy Multigrain Bagel Recipe You’ll Love. Powerful & Easy

These multigrain bagels pack 4 whole grains, oats, flaxseed, wheat germ, and whole wheat, for a chewy, filling bite with real texture. Bake them in under 30 minutes for better flavor than store-bought.

The first time I made these multigrain bagels, I wasn’t trying to outdo the bakery, I just wanted something homemade, hearty, and a little bit special for Sunday morning. What I didn’t expect was how good they’d be: chewy, golden, and filled with the kind of flavor store-bought bagels only pretend to have. Now they’re a weekend staple in our house, and I promise they’ll become one in yours too. No fancy ingredients, no stress, just a warm kitchen and the smell of something real baking in the oven.

Healthy Multigrain Bagel Recipe You’ll Love. Powerful & Easy

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• Author: Betty Thompson
• Total Time: 120 min
• Yield: 290mg 1x

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Description

Soft, chewy multigrain bagels with a golden crust—made from scratch with wholesome ingredients. This foolproof recipe makes bakery-quality bagels right at home, perfect for weekend brunch or meal prep.

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Ingredients

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• 2¼ tsp active dry yeast

• 1½ cups warm water (110°F)

• 2 tbsp brown sugar

• 1½ tsp salt

• 1½ cups bread flour

• 1½ cups whole wheat flour

• ½ cup rolled oats

• ¼ cup ground flaxseeds

• 2 tbsp sunflower seeds

• 1 tbsp olive oil

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Instructions

• In a small bowl, combine warm water and yeast. Let sit for 5–10 minutes until foamy.

• In a large mixing bowl, whisk together flours, oats, flaxseeds, sunflower seeds, salt, and brown sugar.

• Add the yeast mixture and olive oil to the dry ingredients. Mix and knead until smooth and elastic (8–10 minutes).

• Cover the dough and let it rise in a warm spot for about 1 hour or until doubled in size.

• Divide dough into 8 equal pieces. Roll each into a ball, then poke a hole in the center and stretch to form a ring.

• Let shaped bagels rest for 10 minutes. Meanwhile, preheat oven to 425°F and bring a large pot of water to boil.

• Boil each bagel for 1–2 minutes per side. Drain and place on a parchment-lined baking sheet.

• Bake for 20–22 minutes or until golden brown and firm. Cool on a wire rack.

Notes

• Top with oats, sesame, or everything seasoning before baking.

• Freeze sliced bagels for easy weekday toasting.

• Swap sunflower seeds for pumpkin seeds or hemp hearts.

• Prep Time: 20 min
• Rising + Boiling: 100 min
• Cook Time: 20 min
• Category: Protein Bagels, Bread, Breakfast, Baking
• Cuisine: American

Nutrition

• Serving Size: 8 bagels
• Calories: 220
• Sugar: 3g
• Sodium: 290mg
• Fat: 5g
• Saturated Fat: 0.5mg
• Carbohydrates: 40g
• Fiber: 4g
• Protein: 8g
• Cholesterol: 0mg

What Makes a Bagel “Multigrain”?

Multigrain vs. Whole Grain. Wait, What’s the Difference?

Here’s the scoop: multigrain means it’s made with more than one grain (obviously), but that doesn’t always mean they’re whole grains. Whole grains include all parts of the seed, bran, germ, and endosperm, which is where the fiber and nutrition live.

This recipe’s loaded with real-deal grains, whole wheat flour, oats, flaxseed, and wheat germ, all ingredients that bring flavor, fiber, and that hearty chew. That’s what gives our bagels their deep, nutty flavor and that satisfying chew that keeps you full way longer than your average white flour bagel.

Why You’ll Love Multigrain

Once you taste a fresh, homemade multigrain bagel, store-bought won’t cut it. These guys:

• Stay chewy inside, crusty outside
• Have a nuttier, fuller flavor
• Pair beautifully with both sweet and savory toppings
• Are loaded with fiber and plant-based protein

They fit right in on our weekend breakfast table, usually sharing the spotlight with some fresh-milled muffins, juicy fruit, and the kind of chatter that makes you forget the coffee’s gone cold.

Ingredients for Chewy Multigrain Bagels

What You’ll Need (Yields 16 Bagels)

This recipe’s flavor depth is similar to our high-protein lineup, but the texture’s got extra oomph thanks to the grains.

How to Make Multigrain Bagels from Scratch

Step-by-Step Bagel Bliss

You’ll Need:

• 4 large baking sheets
• Mixing bowls
• Large pot for boiling
• Pastry brush
• Clean towel, wax paper, parchment paper, and cornmeal

1. Activate the Yeast

In a small bowl, mix:

• ½ cup warm water (around 105°F – think warm bath, not hot tub)
• 2 (.25 oz) packets of active dry yeast
• ½ teaspoon white sugar

Let it sit for 5 minutes, untouched.

You’re looking for a bubbly foam on top, if it doesn’t foam, toss it and start over (it’s like your dough’s battery won’t charge). This is the step that gives your bagels their chew and rise.

2. Make the Dough

In a very large mixing bowl, stir together:

• 4 cups whole wheat flour
• 2 cups bread flour
• 1 cup rolled oats
• ¼ cup vital wheat gluten
• ¼ cup wheat germ
• ¼ cup organic flaxseed meal
• 1 tablespoon sea salt

Now pour in:

• 3 cups buttermilk
• The yeast mixture you just activated
• ⅓ cup orange blossom honey (or your fave local kind)

Use a wooden spoon or silicone spatula to mix it all until there are no dry patches of flour left. The dough will be dense, sticky, and shaggy, like muffin batter that decided to hit the gym. Let it sit for around 20 minutes, covered loosely with plastic wrap.

3. Knead & First Rise

Sprinkle a little flour on the counter, then flip the dough out like you mean it. Knead by hand for 7 full minutes, press, fold, push, rotate, until the dough is smooth and slightly tacky but not messy.

Pro Tip: If it sticks like crazy, sprinkle in a spoonful of flour at a time, but don’t go overboard, you want a soft, elastic dough.

Spray a clean bowl with cooking spray. Drop the dough in, flip it once to coat, then cover tightly with plastic wrap. Let it rise in a warm, draft-free spot (like inside your turned-off oven) for 2 hours, or until doubled in size.

It should feel airy but still firm, like the dough you use in our protein bagels, but with extra fiber and heft.

4. Shape the Bagels

Turn the dough onto a lightly floured surface. Knead gently for 30 seconds to deflate. Cut the dough in half. Then:

• Roll each half into a long log
• Cut each log into 8 equal pieces
• You’ll have 16 dough balls

Give those bagels a little spa moment, dab the tops with egg wash using your trusty pastry brush. Gently stretch the hole to about 1¾ inches wide.

Repeat with all pieces. Place shaped bagels on a wax-paper lined tray, cover with a towel, and let rest while you prep your boiling setup.

5. Boil for That Signature Chew

Preheat oven to 400°F.

Set up:

• 1 tray with wax paper
• 1 with a clean towel
• 2 trays lined with parchment paper, sprinkled with cornmeal

In a large pot, bring to a boil:

• 3 quarts water
• 1½ tablespoons brown sugar

Once boiling, reduce to a gentle simmer.

Using a slotted spoon or your hands (carefully!), drop in 2 bagels at a time. Boil for 30 seconds per side. They’ll puff up slightly, that’s perfect.

Transfer first to towel-lined tray to drain briefly, then onto cornmeal trays.

This step gives you that shiny, chewy crust, just like the best bakery bagels.

6. Egg Wash & Bake

Whisk together:

• 1 egg white
• 1 teaspoon cool water

Brush the tops of each bagel with the egg wash using a pastry brush.

Bake for 12 minutes, then flip each one with a spatula or tongs. Return to the oven for another 13 minutes, until the bottoms are golden and the tops look deep brown and glossy.

Cool on a wire rack for at least 10–15 minutes, if you can wait.

Nutrition Facts + Healthier Bagel Tips

Nutrition Breakdown (Per Bagel)

Here’s what you’re working with for one of these bakery-style multigrain bagels (based on the tested 16-serving recipe):

📌 These values can vary slightly based on toppings and flour brands, but overall, these bagels bring solid fiber and protein without being calorie bombs.

Are Multigrain Bagels Actually Healthier?

Short answer: Yes, if made right.

Not all multigrain bagels are created equal. Some are just white flour with a few oats slapped on top. But this recipe is made with:

• 100% whole wheat flour base
• Flaxseed, wheat germ, oats, all fiber-rich whole grains
• Honey instead of refined sugar
• Buttermilk for a soft texture and added calcium

If you’re looking for a morning bite that keeps you full and supports digestion, these beat plain bagels or store-bought imposters by a mile.

They’re the perfect swap if you’re used to grabbing a bagel and coffee on the run, but want something that won’t leave you crashing by 10 a.m. (Try pairing one with a blueberry protein muffin on Sunday and have grab-and-go breakfasts all week.)

Smart Toppings for Multigrain Bagels

Some combos we love:

• Savory: Veggie cream cheese, avocado + tomato, or sharp cheddar + scrambled eggs
• Sweet: Almond butter + banana, ricotta + figs, a cinnamon-raisin mash-up (yep, we turn leftovers into spreads around here).

For high-protein toppings, try cottage cheese, smoked salmon, or a soft-boiled egg sliced thin. These all bring balance to the bagel’s carb-rich base.

You can also slice and toast the bagel, then top it like a mini open-faced sandwich, we do this with leftovers when we’ve got protein muffin crumbs on the counter and want a power snack.

Betty’s Bagel Tips (aka What I Messed Up So You Don’t Have To)

• Don’t over-knead, 7 minutes is your sweet spot. More = dense.
• If your bagels deflate in the boil, your rise may have gone too long.
• That hole in the middle? Stretch it bigger than you think. It’ll shrink during boiling + baking.
• Use a damp towel while shaping to keep them from drying out.

Mia once made a batch where the holes sealed shut completely. Jordan called them “pillow breads.” Still tasty. Still got eaten.

Multigrain Bagel FAQ