Easy Whole Wheat Sourdough Bagels: Tangy, Chewy & Freshly Milled for Optimal Flavor
Prepare to be amazed by these incredible Whole Wheat Sourdough Bagels, featuring a uniquely tangy and delightfully chewy crust that’s truly irresistible. This recipe is designed for ease and convenience, allowing you to create a batch of these wholesome bagels on the same day you start them. Crafted with nutrient-rich freshly milled whole wheat flour and an active, bubbly sourdough starter, these aren’t just good bagels – they’re the best! Enjoy them fresh from the oven, or stock your freezer for quick, delicious meals anytime. We especially love them adorned with our savory, homemade everything bagel seasoning for an extra burst of flavor.
Sourdough bagels have quickly become one of my absolute favorite ways to utilize an active sourdough starter. Regularly feeding my starter means I always have a healthy, thriving culture ready to transform into delightful baked goods. Beyond these incredible bagels, I often rotate between baking a hearty Whole Wheat Sourdough Sandwich Bread or light and airy Sourdough English Muffins. The versatility of sourdough is truly unmatched, and these bagels showcase its unique qualities beautifully.
Wholesome Goodness: The Benefits of Whole Wheat Sourdough Bagels
While traditional sourdough bagels are fantastic, incorporating whole wheat flour elevates them to a new level of health and flavor. These whole wheat sourdough bagels are just as quick to prepare as their conventional counterparts, with the added benefit of being significantly healthier. Opting for whole grains, especially freshly milled, offers a wealth of advantages over typical store-bought white flour. Whole grains retain all parts of the wheat kernel – the bran, germ, and endosperm – which means they are packed with fiber, essential vitamins, and minerals that are often stripped away in refined flours.
By starting your day fermenting freshly milled grains, you not only allow the flavors to deepen and mature but also make the bagels easier to digest. The sourdough process breaks down complex carbohydrates and gluten, transforming them into a more gut-friendly food. Imagine baking these nourishing bagels in the evening, ensuring you have a wholesome and satisfying breakfast or lunch ready for the next day. It’s a simple shift that makes a big difference in your daily nutrition.
Sourdough Bagels: Why No Commercial Yeast?
What makes these bagels truly special is their reliance solely on the active yeast present in your sourdough starter. There’s no need for commercial yeast or other leavening agents here. Your starter acts as a natural powerhouse, providing both the rise and a host of gut-friendly benefits. This natural fermentation process, combined with the goodness of freshly milled grains, results in a super wholesome and nutrient-dense food that you can feel great about eating and serving to your family.
The Power of Freshly Milled Flour
Milling your own fresh flour is a game-changer for baking. It produces a remarkably flavorful, highly digestible, and incredibly nutritious product. I personally rely on this efficient grain mill, which transforms whole grains into fresh flour in mere seconds. When I mill my own flour, I know I’m retaining all the vital components of the wheat kernel: the bran, which is packed with fiber; and the wheat germ, a treasure trove of nutrients including vitamin B6, folate, thiamin, zinc, magnesium, manganese, and vitamin E. This ensures that every bagel you bake is not just delicious but also a powerful source of essential nutrition.
Beyond the enhanced flavor, these bagels are a fantastic way to fuel your body and stay energized during busy mornings. The rich fiber content in whole wheat helps you feel fuller for longer, preventing those mid-morning slumps and keeping you satisfied until your next meal. It’s a truly delicious and satisfying start to any day.
The type of wheat berries you choose can influence the appearance and subtle flavor of your bagels. When using a lighter grain like hard white wheat, your sourdough bagels will have a delicate, ever-so-lightly tinted hue and a milder taste. In contrast, hard red wheat will produce a more robust flavor profile and a darker, richer color. Experimenting with different grains can be a fun way to customize your bagel baking!
If the idea of making bagels from scratch feels intimidating or overly daunting, let me reassure you – it’s far easier than it seems! My stand mixer handles the majority of the work, taking the effort out of kneading. My primary tasks involve shaping the dough and giving them a quick boil in water just minutes before baking. The rest of the process is largely hands-off, allowing you to enjoy the process without excessive fuss.
My kids adore these bagels plain or generously slathered with cream cheese and sweet Strawberry Jam. For my part, I love to dress them up with homemade everything bagel seasoning or sprinkle on minced onions. These toppings not only add incredible flavor but also contribute extra nutrients from various seeds and spices. Below, I’ll delve into a few different variations and offer more ideas for delicious bagel sandwiches.
Baking with whole grains, especially freshly milled flour, requires a slightly different approach than working with refined white flour. A kitchen scale is an essential tool to accurately weigh the precise amount of flour needed. Freshly milled whole wheat flour absorbs liquid more slowly than white flour dough, making visual estimation unreliable. I typically weigh my whole grains before running them through my grain mill; this ensures the exact amount of flour required for the recipe.
How To Make Sourdough Bagels with Freshly Milled Flour
Crafting these delectable sourdough bagels requires attention to detail, but the process is straightforward and rewarding. Bagel dough is inherently very stiff, making a stand mixer an invaluable tool for the job. Attempting to knead this dough by hand would be incredibly tiresome! The secret to achieving that signature chewy texture in a whole wheat bagel is to knead the dough for a full 25 minutes. This extended kneading time is crucial for properly developing the natural gluten in the whole wheat flour. You’ll know the dough is ready when it passes the “window pane test” – meaning you can stretch a small piece of dough thin enough to see light through it without tearing – and when the dough feels smooth and very pliable.
- **Prepare Your Starter:** Ensure your sourdough starter is active and bubbly. I recommend feeding it the night before you plan to bake to ensure maximum activity.
- **Mix the Dough:** In the morning, it’s time to make the bagel dough. Using a stand mixer fitted with the dough hook attachment, combine all the dough ingredients: warm water, freshly milled whole wheat flour, salt, honey, and your active sourdough starter. Knead the mixture on low speed (typically speed 2 on a KitchenAid mixer) for a full 25 minutes. The dough should transform into a smooth, elastic, and pliable mass.
- **First Fermentation (Bulk Ferment):** Once kneaded, cover the dough securely with plastic wrap or a reusable beeswax wrap. Allow the dough to ferment in a warm spot for 6-8 hours. During this time, the sourdough starter will work its magic, developing flavor and rise.
- **Divide the Dough:** After the dough has fermented and noticeably risen, gently transfer it to a large silicone pastry mat or a lightly floured work surface. Divide the dough into 8 equal pieces. For best results and consistent bagel sizes, a kitchen scale is recommended here.
- **Shape the Bagels:** Roll each piece of dough into a tight ball. Then, using your finger, poke a hole directly in the middle of each ball. Gently stretch out this hole to widen the bagels, aiming for a consistent ring shape.
- **Second Rise (Proofing):** Arrange the shaped bagels on a silicone-lined baking sheet, ensuring they are spaced apart. Allow them to rise for up to 2 hours in a warm environment. The exact time may vary depending on the warmth of your kitchen – a warmer spot will speed up the proofing.
- **Prepare for Boiling:** Preheat your oven to 425°F (220°C). While the oven heats, bring a large pot (or Dutch oven) filled with approximately 12 cups (3 quarts) of water to a rolling boil. Once boiling, add the baking soda and brown sugar to the water. This step is crucial for developing the bagels’ signature chewy crust and helps with browning.
- **Boil the Bagels:** Carefully drop the bagels into the boiling water, 4 at a time, to avoid overcrowding the pot. Boil for 60 seconds on each side. Use a slotted spoon or spider strainer to gently flip them over.
- **Add Toppings:** After boiling, place the bagels back onto a clean silicone-lined baking sheet. This is the perfect time to dip them into your desired toppings – whether it’s everything bagel seasoning, sesame seeds, or a sweet cinnamon-sugar mixture. Arrange the topped bagels about 2 inches apart on the pan.
- **Bake to Perfection:** Transfer the baking sheet to the preheated oven. Bake for 20-25 minutes, or until the bagels are beautifully golden brown and boast a firm, chewy crust.
Creative Add-ins and Serving Suggestions for Sourdough Whole Wheat Bagels
These versatile sourdough whole wheat bagels are perfect on their own, but they also serve as an excellent canvas for various flavors and fillings. Here are some yummy ways to enjoy them, along with creative add-ins you can incorporate directly into the dough before shaping:
- **Sweet Inclusions:** For a sweet treat, gently knead in dried blueberries, rich chocolate chips, or a classic combination of cinnamon and plump raisins into the dough before shaping.
- **Savory Topping Ideas:**
- Transform your bagels into spicy and savory Jalapeno Cheddar bagels by topping them with shredded cheddar cheese and thinly sliced fresh or pickled jalapenos after boiling.
- Craft your very own “everything bagel seasoning” by mixing equal parts dried minced onion, dried minced garlic, poppy seeds, and sesame seeds. Press the boiled bagels into this mixture for that iconic flavor.
- For a comforting sweet variety, mix brown sugar and cinnamon and sprinkle it generously over the bagels after they’ve been boiled, then bake as directed.
- **Enhanced Cream Cheese:** Elevate your cream cheese by stirring in a touch of vanilla extract or a drizzle of maple syrup for a delightful sweetness.
- **Classic Lox Sandwich:** Create an exquisite sandwich with rich cream cheese and savory salmon lox. For an added layer of flavor and crunch, I love to include thinly sliced purple onions.
- **Versatile Lunch Sandwiches:** Use your favorite lunch meats to build wholesome and delicious bagel sandwiches, complete with fresh greens. A quick and satisfying idea includes cream cheese, thinly sliced salami, and a fresh arugula salad mix. For the ultimate comfort food, I adore bagels with creamy mayonnaise, a perfectly fried egg, and a slice of melted American cheese – simply irresistible!
How To Store Whole Wheat Sourdough Bagels
Proper storage is key to keeping your homemade sourdough bagels fresh and delicious. If stored in an airtight bag at room temperature, these bagels will maintain their quality for up to a week. However, if your home is particularly warm, it’s best to store them in the refrigerator to prolong their freshness. They also tend to develop an even better texture once toasted, making them perfect for reheating.
Since I often make multiple batches, freezing is my preferred method for long-term storage. To freeze bagels, ensure they have cooled completely to room temperature. Then, stack about 8 bagels at a time in a dedicated plastic bread bag or a freezer-safe container. Frozen bagels can be kept in the freezer for up to 3 months without losing quality. For added convenience and to save time later, consider slicing them before freezing. This allows you to easily toast them directly from frozen or with minimal thawing.
Q&A: Your Sourdough Bagel Questions Answered
Can I Use Store-Bought Whole Wheat Flour for This Recipe?
This sourdough bagel recipe has been specifically developed for use with freshly milled flour. Store-bought whole wheat flour differs significantly from freshly milled flour. Over time, as commercial flour sits on the shelf, it loses some of its delicate nutrients and natural oils. Additionally, commercially available whole wheat flour is often made from hard red wheat varieties unless explicitly stated otherwise. I prefer using hard white wheat for its milder taste and lighter color, which yields a slightly different result in the finished bagel. While you *could* try store-bought, be aware that the texture and flavor might vary.
Are All Bagels Sourdough?
Not all bagels are sourdough, but sourdough is a key ingredient in creating the distinctive qualities often associated with premium bagels, like those found in New York. Sourdough doesn’t just help the dough rise; it also imparts an incredibly chewy crust and a characteristic tangy taste that makes sourdough bagels stand out from other types of bread. Many “New York-style” bagels, even if not explicitly labeled sourdough, often contain enzymes that mimic the effects of sourdough fermentation. While you can certainly make bagels with commercial yeast, the resulting texture will typically be more bread-like and lack the deep chewiness that sourdough provides.
Why Are Bagels Boiled Before Baking?
Boiling bagels before baking is a crucial step that contributes significantly to their unique texture and appearance. This brief dip in boiling water helps to set the crust, preventing the bagels from rising too much in the oven and resulting in that dense, chewy interior. The addition of baking soda in the boiling water helps produce a thicker, glossier crust and aids in browning during baking. I use one tablespoon of baking soda and one tablespoon of brown sugar for a medium-brown crust; if you prefer darker bagels with an even richer color, you can increase the amount of baking soda in your boiling water.
Can I Make Whole Wheat Bagels with Sourdough Discard?
Yes, you can absolutely adapt this recipe to make “sourdough discard bagels” if your sourdough starter is weak, unfed, or you simply want to use up discard. To do this, you’ll need to supplement the lack of active yeast in your discard by adding commercial yeast to the bread dough before kneading. Typically, one tablespoon of dry active yeast is recommended for every 560 grams of flour. This will provide the necessary leavening for a good rise while still incorporating the flavor and digestibility benefits of your sourdough discard.
Are Sourdough Bagels Healthy?
This whole wheat sourdough bagel recipe is indeed very nutritious, thanks to the combination of freshly milled whole grains and the natural fermentation process of sourdough. Freshly milled whole grains are a complete source of fiber, vitamins, and minerals. Sourdough fermentation further enhances the health benefits by breaking down starches and anti-nutrients, making the grains easier for your body to digest and absorb nutrients. This results in a wholesome and highly beneficial baked good.
Expert Tips for Making Perfect Whole Wheat Sourdough Bagels:
- **Avoid Over-Fermentation:** Be mindful of fermentation times. If you observe any excess liquid seeping from the dough, it’s a sign of over-fermentation. Freshly milled flour doughs typically do not fare well with overnight refrigeration for the bulk ferment. This type of dough is heavier and ferments slower, and bringing it back to room temperature takes considerably longer. For optimal results, I find it works best when fermented at room temperature and baked on the same day.
- **Prioritize Freshly Milled Flour:** For the best flavor and nutritional profile, freshly mill your own flour using a good quality grain mill and organic whole grains. I specifically recommend hard white wheat for bagels, as it produces a lighter-colored bagel with a mild, pleasing flavor. Azure Standard is an excellent source for organic whole grains.
- **Use a Robust Stand Mixer:** Bagel dough is notoriously stiff. I use a heavy-duty professional KitchenAid HD stand mixer, which handles a single batch perfectly. If you are using a less powerful mixer or making a double batch, your mixer might overheat. To prevent this, stop the mixer halfway through the kneading time and allow it to rest for 10 minutes before resuming.
- **Keep Dough Covered:** Always cover your dough thoroughly with a wet tea towel, plastic wrap, or beeswax wrap. This prevents a dry skin from forming on the surface of the dough, which can impede rising and lead to a crusty exterior prematurely.
- **Boiling Best Practices:** Add the baking soda and brown sugar to the water only *after* it has reached a rolling boil. When boiling the bagels, drop them in four at a time to prevent overcrowding the pot, which can lower the water temperature and result in uneven boiling.
- **Easy Retrieval:** Use a slotted spoon or a spider strainer to easily remove and drain the boiled bagels from the hot water. This ensures they don’t absorb too much water and helps maintain their shape.
- **Extended Kneading for Whole Wheat:** Recipes using freshly milled flour, particularly whole wheat, require longer kneading times than those made with refined flours. This extended kneading (up to 25 minutes) is essential to properly develop the gluten structure, resulting in a pliable dough and the desired chewy texture. Whole wheat flour also absorbs liquid more slowly, so allow ample time for the dough to fully hydrate.
- **Grain Variety:** Feel free to experiment with different types of whole grains. You can mix in or substitute with grains like spelt, einkorn, or kamut for unique flavor profiles and textures.
- **Sourdough Discard Option:** This whole wheat sourdough bagel recipe can indeed be made with an unfed or discarded starter. Simply add 1 tablespoon of dry active yeast to the dough along with the other ingredients before kneading to ensure a proper rise.
- **Same-Day Baking:** For the freshest and most predictable results, begin your dough in the morning so you can bake your delicious bagels on the same day.
- **Fermentation Benefits:** Remember, the longer the fermentation time (within the recommended range), the more beneficial the bagels are for digestion and nutrient absorption.
More Sourdough Recipes to Explore:
Whether you’re new to sourdough baking and need a beginner-friendly recipe or are looking for a staple sourdough sandwich bread loaf, I’ve got you covered! Here are some of my favorite sourdough recipes to inspire your next baking adventure:
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Sourdough Bagels
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Whole Wheat Sourdough Bread (Boule)
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No-Knead Sourdough Bread
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Sourdough French Bread
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Whole Wheat Sourdough Sandwich Bread with Freshly Milled Flour
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Where To Buy Sourdough Starter
-
Sourdough English Muffins
-
Moist Whole Wheat Bread Loaves Recipe

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Whole Wheat Sourdough Bagels
Equipment
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1 large pot for boiling bagels
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1 18×13″ sheet pan
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1 Stand Mixer
Ingredients
Ingredients:
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1 1/4 cup warm water (267 grams)
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1 cup sourdough starter (218 grams of active and bubbly starter)
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2 Tbsp honey (21 grams)
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2 tsp salt (10 grams)
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560 grams hard white wheat berries (about 4 cups of freshly milled flour)
For Boiling the Bagels:
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3 quarts water
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1 Tbsp baking soda
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1 Tbsp brown sugar
Instructions
Directions:
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Weigh the grains and run them through a grain mill to mill the flour.
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In the bowl of a stand mixer combine all the dough ingredients in the order given. Knead over low speed for 25 minutes.
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Cover the bowl with plastic wrap and allow the dough to ferment for 6-8 hours in a warm spot.
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After the dough has fermented, transfer the dough to a work surface and divide it into 8 equal pieces.
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Roll the dough into balls and poke a hole in the middle with your finger. Stretch out the hole to widen the bagels.
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Place bagels on a silicone-lined baking sheet and allow the dough to rise for up to 2 hours in a warm spot.
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Preheat the oven to 425°F and bring a large pot of water to a boil. Add the baking soda and brown sugar. Drop the bagels in four at a time and boil for 60 seconds on each side.
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Place the bagels over a silicone-lined baking sheet. Dip into toppings of choice and arrange 2 inches apart on the pan.
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Bake for 20-25 minutes or until golden brown.
Notes
- To make everything bagel seasoning: combine 2 tablespoons each of dried minced onions, minced garlic, poppy seeds, and sesame seeds. Dip wet bagels into the mixture on both sides then arrange on pan.
- Dip the bottoms of the bagels with bagel seasoning so they don’t stick or use parchment paper.
- If making a double batch of bagels stop the mixer halfway between the kneading time so the mixer doesn’t overheat. Unless you’re using a heavy-duty mixer.
Nutrition per serving