A good bagel starts with good flour.
When that flour is milled fresh, something remarkable happens – the dough comes alive with flavor, aroma, and texture that simply feels right.
Each bite carries the wholesome character of freshly ground grains, creating a bagel that’s pleasantly chewy with a golden crust and a naturally satisfying taste.
This recipe is designed for home bakers who appreciate clarity, balance, and real ingredients.
Once you taste the difference fresh milled flour makes, it just makes sense to keep a batch of these on your counter.
Jump to the Recipe
If you’re ready to start baking right away or just want a quick reference for ingredients and steps, click here to go straight to the Quick Recipe Card at the bottom of this post.
But if you want the full, complete guide – with tips for perfect bagel texture, storage advice, and troubleshooting – keep reading.
Everything you need to make bakery-level bagels at home is right here!
Why You Should Use Freshly Milled Flour
Freshly milled flour is exactly what it sounds like – flour made right after the grain is ground.
When you use it right away, you’re working with all the natural oils, nutrients, and flavor that are still alive in the grain.
Nothing’s been sitting on a shelf, and nothing’s been processed to last longer than it should.
You’ll notice the difference right from the mixing bowl. The dough feels smoother, smells richer, and rises with steady strength.
Fresh flour still has the wheat’s natural balance of bran, germ, and endosperm – everything that gives bread its honest character.
There’s also a practical side. Milling your own flour lets you choose your grain and grind size, so you’re in full control of your ingredients.
You can keep it hearty with hard red wheat or make it softer with white wheat – it’s up to you.
I swear, once you see how it performs in bagels, you’ll start reaching for it for everything from pancakes to sandwich loaves (and even sugar cookies with fresh milled flour).
Essential Ingredients for Perfect Homemade Bagels
Here’s what you’ll need to make bagels that taste like they came straight from a cozy bakery – only better, because they’re made right at home.
Makes 8 Bagels
- 4 cups (520g) freshly milled hard white or hard red wheat flour
- 1 ¼ cups (295ml) warm water
- 2 teaspoons instant yeast
- 1 tablespoon honey
- 1 ½ teaspoons salt
- 1 tablespoon barley malt syrup (optional)
- For boiling:
- 8 cups (1.9L) water
- 1 tablespoon honey or malt syrup
- For topping (optional): sesame seeds, poppy seeds, or coarse salt
Tools That Make Bagel-Making Easier
- Mixing bowl
- Kitchen scale
- Dough scraper
- Clean kitchen towel or plastic wrap
- Slotted spoon
- Baking sheet and parchment paper
- Cooling rack
- Grain mill (optional) – If you plan to bake often, a home grain mill makes fresh flour simple to keep up with.
How to Make the Ultimate Homemade Bagels (Step-by-Step Guide)
Now, grab your favorite apron, and let’s make some bagels that’ll fill your kitchen with the best kind of bakery smell!
1. Mill the Flour
Start by milling your whole wheat berries right before you bake.
Use a fine to medium grind – this keeps the dough strong but not heavy.
For tips on choosing the right grain and getting the best results, check out freshly milled flour for beginners. It’s packed with guidance to make your bagels taste incredible.
Measure 4 cups (520g) after milling, not before, since fresh flour can settle differently.
If you don’t have a grain mill, you can still follow this recipe using high-quality whole wheat flour, but the flavor and texture shine brightest when it’s freshly milled.
2. Mix and Knead the Dough
In a large bowl, mix 1¼ cups warm water, 2 teaspoons instant yeast, and 1 tablespoon honey. Stir until the yeast and honey dissolve.
Add about three-quarters of your flour and 1½ teaspoons salt. Use a sturdy spoon or your hands to combine until a shaggy dough forms.
Add the rest of the flour a little at a time.
When the dough starts to hold together, transfer it to a lightly floured surface and knead for about 8–10 minutes.
The dough should feel firm and elastic – soft enough to shape, but strong enough to bounce back when pressed gently.
If it’s sticking too much, dust your hands lightly with flour.
Avoid adding too much extra flour though; the dough should stay moist and supple.
3. First Rise (About 1 Hour)
Lightly oil a clean bowl and place the dough inside, turning it once to coat the top with oil.
Cover with a clean towel or plastic wrap and let it rise in a warm spot for about 1 hour.
You’re looking for the dough to puff up slightly – not necessarily double in size.
Press it gently with a fingertip; if it springs back slowly, it’s ready for shaping.
Want to take your baking further? Learn how to make a sourdough starter with freshly milled flour and start creating naturally leavened breads at home.
4. Shape the Bagels
Turn the dough out onto a lightly floured surface and divide it into 8 equal pieces.
A kitchen scale helps here, but eyeballing works fine. Roll each piece into a smooth ball by tucking the edges underneath.
To shape, poke your thumb through the center of a ball, then gently stretch it outward until the hole is about 2–3 inches wide.
The dough will shrink back a little as it rests – that’s normal. Arrange the shaped bagels on a parchment-lined baking sheet.
If you like a smoother crust, cover them with a damp towel for a few minutes while you finish shaping the rest.
5. Second Rise (20–30 Minutes)
Once all your bagels are shaped, cover them again with a towel and let them rest for about 20–30 minutes.
This brief rise helps the dough relax, which makes the bagels lighter and easier to handle when boiling.
When you gently touch one, it should feel soft but still spring back slightly.
6. Boil the Bagels
Bring 8 cups of water to a gentle boil in a large pot.
Stir in 1 tablespoon of honey or barley malt syrup – this gives the bagels their subtle sweetness and signature shine.
Carefully lower 2–3 bagels into the boiling water at a time. They should float within a few seconds.
Boil for 30 seconds per side to develop that chewy texture. If you prefer a thicker crust, you can go up to 45 seconds per side.
Use a slotted spoon to lift them out and let excess water drip off.
Return them to the parchment-lined sheet, keeping them evenly spaced.
7. Add Toppings (Optional)
While the bagels are still damp from boiling, sprinkle on your favorite toppings – sesame seeds, poppy seeds, everything seasoning, or coarse salt.
The moisture helps everything stick naturally.
If you’re keeping them plain, a quick brush of egg wash (1 egg mixed with 1 tablespoon of water) adds a nice golden shine when baked.
8. Bake
Preheat your oven to 425°F (220°C).
Slide the tray into the center rack and bake for 20–25 minutes, until the bagels are evenly golden and firm on top.
You’ll know they’re done when they sound hollow if you tap the bottom and the surface has a light sheen.
Move them to a cooling rack right away to prevent steam from softening the crust.
9. Cool and Enjoy
Let the bagels cool for at least 10 minutes before slicing.
The inside continues to set as they rest.
Once cooled, they’re ready for butter, cream cheese, or anything you like.
The texture should be pleasantly chewy, the crust crisp, and the flavor clean and full – the kind of result that comes from working with fresh, honest ingredients.
Looking for another way to enjoy freshly milled flour? Check out how to make sugar cookies with fresh milled flour for a sweet, buttery treat that highlights the flavor and texture of your homemade grains.
6 Proven Tips to Get the Perfect Bagel Texture Every Time
A good bagel has that balance – chewy on the inside, crisp on the outside, and full of flavor that holds up even after toasting.
These small details turn a basic batch into one that feels like it came from your own neighborhood bakery.
1. Mind Your Flour-to-Water Balance
Fresh milled flour absorbs water differently than store-bought flour.
Some grains soak up more moisture depending on their age or type.
Start with the water in the recipe, then adjust by a tablespoon at a time if the dough feels too stiff or too sticky.
You’re aiming for a dough that feels firm but still easy to knead – a dough that holds shape without crumbling.
Once you feel that texture, you’ll recognize it every time.
If you’re adjusting older recipes, you might find this guide on how to convert any recipe to freshly milled flour helpful.
2. Knead Until the Dough Feels Alive
This is the part where your hands teach you. Bagel dough should be strong and springy.
As you knead, it will shift from rough to smooth and elastic. If you press it lightly and it bounces back, that’s when you know it’s ready.
A little patience here makes all the difference in chew and structure later.
3. Keep an Even Rise
Yeast loves consistency.
Let your dough rise somewhere steady—not too warm, not too cool. Around 75°F (24°C) is a sweet spot for most kitchens.
If your kitchen runs cooler, give it extra time instead of extra heat. The dough should puff gently, not rush.
4. Don’t Skip the Boil
That short boiling step is what separates a bagel from a bread roll. Boiling sets the crust and locks in the chew.
If you want a bagel that’s firm but not tough, keep your water at a steady simmer (not a rapid boil) and don’t overdo the time.
The honey or malt syrup in the water gives that classic shine and light sweetness, so it’s worth adding.
5. Bake All the Way
Bagels need steady, strong heat to build their crust.
If your oven has hot spots, rotate the tray halfway through. You’re looking for a deep golden color, not pale or overly dark.
Let them cool on a rack so the crust stays crisp. If you leave them on the tray, the steam underneath will soften the bottoms.
6. Use Freshness to Your Advantage
Fresh milled flour brings natural oils and nutrients that store-bought flour can’t match, but those oils also mean it’s best to use right away.
Try to mill just what you need for the recipe.
That freshness is what gives your bagels their clean, hearty flavor – it’s worth the small bit of planning.
Quick Recipe Card: Homemade Bagels with Freshly Milled Flour
Makes: 8 bagels
Prep Time: 30 min
Rise Time: 1 hr + 20–30 min
Cook Time: 20–25 min
Ingredients
Bagel Dough
- 4 cups (520g) freshly milled hard white or hard red wheat flour
- 1 ¼ cups (295ml) warm water
- 2 tsp instant yeast
- 1 tbsp honey
- 1 ½ tsp salt
- 1 tbsp barley malt syrup (optional)
For Boiling
- 8 cups (1.9L) water
- 1 tbsp honey or malt syrup
Toppings (optional)
- Sesame seeds, poppy seeds, coarse salt
Quick Steps
- Mill Flour: Fine to medium grind; measure 4 cups (520g).
- Mix & Knead: Combine water, yeast, honey; add flour + salt gradually; knead 8–10 min until elastic.
- First Rise: Oil bowl, cover dough, let rise ~1 hr until puffed.
- Shape Bagels: Divide into 8, roll balls, poke center, stretch 2–3 in; place on parchment-lined tray.
- Second Rise: Cover, rest 20–30 min.
- Boil: Boil 2–3 bagels at a time, 30 sec per side in water + honey/malt.
- Toppings: Sprinkle while damp or brush with egg wash for plain bagels.
- Bake: 425°F (220°C) for 20–25 min until golden; cool on rack 10+ min.
Tips: Chewy inside, crisp outside; adjust water slightly for fresh-milled flour; boil for classic bagel crust; enjoy plain or with toppings.
If you love baking with fresh grains, you might also enjoy this best shoofly pie you’ll ever taste!
How to Keep Homemade Bagels Fresh + Simple Serving Ideas
Fresh bagels are at their best on the day they’re baked, but that doesn’t mean they lose their appeal later.
With a few simple habits, you can keep that great texture and flavor for days – or even weeks if you freeze them properly.
Storing Fresh Bagels
Let your bagels cool completely before you store them. If they’re still warm, steam gets trapped inside and softens the crust.
Once cooled, place them in a paper bag first, then slip that into a plastic bag or airtight container.
The paper keeps the crust from turning soggy, while the outer bag helps prevent them from drying out.
At room temperature, they’ll stay fresh for about 2 to 3 days. If you plan to keep them longer, freezing is the better route.
Freezing for Longer Storage
Slice the bagels in half before freezing – it makes reheating easier later.
Wrap each one tightly in plastic wrap or parchment, then place them all in a freezer-safe bag.
Remove as much air as possible before sealing.
They’ll keep their quality for up to 3 months in the freezer.
When you’re ready to enjoy one, just pop it in the toaster straight from frozen or warm it in the oven for a few minutes.
Reheating for Best Texture
To bring back that freshly baked feel, lightly mist or brush the cut side with a touch of water before toasting.
It helps revive the crust without drying out the inside.
For a softer bagel, wrap it in foil and warm it in a 300°F (150°C) oven for about 8–10 minutes.
Serving Ideas
Bagels are easy to fit into any part of the day. Here are a few simple ways to enjoy them:
- Classic: Toasted with cream cheese or butter – simple and always satisfying.
- Savory: Layered with eggs, cheese, and vegetables for a hearty breakfast sandwich.
- Sweet: Spread with nut butter and sliced fruit for a balanced snack.
- Creative: Cube and toast leftovers for homemade bagel croutons.
A homemade bagel holds up well to any topping or filling, but its real strength is how it stands on its own!
Bake Your Own Batch This Week!
Making homemade bagels with fresh milled flour just takes some practice and attention.
Once you’ve gone through the process, you’ll see how repeatable it really is.
The steps become familiar, the results consistent, and your kitchen starts to smell like a place where good food happens often.
The best part is knowing exactly what’s in your bagels – flour you milled yourself, ingredients you trust, and flavor that stands on its own.
Whether you’re baking for breakfast, meal prep, or simply because you enjoy it, these bagels fit easily into real life.
If you try this recipe, I’d love to hear how it goes – share your results, adjustments, or favorite toppings in the comments below.
Your experience might help the next person give it a try!
FAQs
1. Can I use all-purpose flour instead of fresh milled flour?
Yes, you can. The recipe will still work, but the flavor and texture will be slightly different. All-purpose flour gives a smoother, lighter crumb, while fresh milled flour adds a fuller flavor and denser chew. If using all-purpose, keep the water amount the same and expect a slightly softer dough.
2. What type of wheat works best for bagels?
Hard white or hard red wheat is ideal because they have higher protein content, which supports gluten development and gives bagels their structure. Hard white wheat produces a milder flavor; hard red brings a deeper, nuttier taste. You can also mix the two for balance.
3. How do I know if my dough has been kneaded enough?
A well-kneaded dough will feel smooth, firm, and slightly elastic. When you stretch a small piece between your fingers, it should form a thin “windowpane” without tearing easily. That means the gluten is fully developed, and the dough is ready to rise.
4. Can I make the dough the night before?
Yes. After kneading, cover the dough tightly and refrigerate overnight. The slower rise enhances flavor and makes the morning process easier. When you’re ready to shape, let the dough sit at room temperature for 30–40 minutes before forming the bagels.
5. How can I tell if the bagels are fully baked?
Look for an even golden crust and a firm feel when you gently press the top. The bottoms should sound hollow when tapped. If you’re unsure, you can check the internal temperature – it should read around 200°F (93°C) when fully baked.
