NY Style Bagels – How To Make With Fresh Milled Flour
How To Make NY Style Bagels with fresh milled flour. As well as achieving the perfect chewy texture and distinctive flavor that have made New York bagels a worldwide sensation. There are a few tricks I want to share with you. So, let’s go through the step-by-step process of creating these beloved bagels from the comfort of your home.

Do I Have To Overnight Ferment My Bagels?
The overnight ferment step is not required, you can proceed with the recipe without it. However, I highly recommend trying it at least once. Plus, this step actually makes it so much more convenient for fresh bagels in the morning. I do all the kneading, rising, shaping the evening before. Then, they rest in the fridge overnight. The next morning all I have to do is boil and bake them! I am no necessarily a morning person, so this little trick is such a wonderful one for me!

Also, the overnight ferment will allow the bagel flavor to intensify and get that slight tang flavor, even without sourdough. And that beautiful blistering the skin of the bagels have, yep, that is also intensified by the overnight rise in the fridge. So, even though this recipe is a yeast recipe, and not a sourdough one, the overnight ferment time dramatically enhances these bagels tremendously. If you are looking for a sourdough bagel recipe instead, HERE is one that is yummy from Lisa at Farmhouse on Boone.
How Long Do I Boil The Bagels For?
Although in my video I only boiled the bagels for 20 second on each side. Since then, I have realized the bagels benefit from a slightly longer boiling time. So, I would recommend boiling the bagels for about 40 second on each side for a total of close to a minute and a half. Then, they are ready to be baked. I recommend you bake these at a high temperature, I will go over that in the baking instructions down below.

Do I Have To Use Malt?
In the realm of NY Style Bagel perfection, one key ingredient reigns supreme: malt. The secret to achieving that signature chewiness and golden-brown blistery crust lies in the incorporation of malt into your bagel recipe. Malt extract, whether in syrup or powder form, holds the power to transform ordinary dough into an extraordinary culinary experience. Its natural sugars not only enhance the bagels’ crust color but also play a crucial role in developing that distinctive depth of flavor we associate with the classic New York bagel. HERE is the kind I use.
However, if you do not have malt, and don’t have time to get any there are a couple substitutions that will work, just not ‘quite’ the same. Here are some alternatives, but do make note, I recommend you try the malt at some point and see the difference, and which you prefer:
- Molasses
- Brown Sugar
- Sucanat
- Honey

What Are Some Good Flavors To Add To My Bagels Made With Fresh Milled Flour?
There are so many flavor options you could choose to make these bagels even more flavorful! Try one of your own or here are a few ideas to start with:
- Everything Bagel: A timeless favorite, this bagel is generously coated with a blend of poppy seeds, sesame seeds, dried garlic, dried onion, and coarse salt, delivering a harmonious symphony of savory flavors. Many stores now carry this delicious concoction already mixed too for convenience sake!
- Cinnamon Raisin: Embrace a touch of sweetness with a dash of ground cinnamon and a scattering of plump raisins within the dough. Perfect toasted with cream cheese or butter.
- Sesame Seed: Keep it simple and elegant by generously coating the bagel with nutty sesame seeds. The toasted seeds provide a delightful crunch and a subtle, earthy flavor.
- Garlic Parmesan: Infuse your bagel with rich, roasted garlic and a sprinkle of grated Parmesan cheese for an indulgent and aromatic twist on the classic.
- Blueberry: Transform your bagel into a breakfast delight by gently folding in fresh or dried blueberries into the dough. A drizzle of honey or a smear of cream cheese complements the fruity essence.
- Jalapeño Cheddar: Add a hint of heat with finely chopped jalapeños and a generous sprinkling of sharp cheddar cheese. This bagel packs a flavorful punch and is perfect for those who crave a little kick.
- Asiago Cheese: Top your bagel with Asiago cheese, and experience with the robust and nutty notes of Asiago cheese
Ingredients To Make Bagels With Fresh Milled Flour
- 4 Cups of fresh milled flour 480g (I milled 400g of hard white wheat berries & 80g of Kamut berries to get this amount.)
- 2 tsp salt
- 1 TBSP Malt syrup (you could use molasses or brown sugar if needed instead)
- 1&1/4 cup warm water 295g
- 1&1/2 tsp instant yeast
Water Bath Ingredients (the next morning)
- 2 quarts of water 2000g
- 2 TBSP malt syrup (you could use molasses or brown sugar if needed instead)
- 1 TBSP sugar
Optional Toppings – you could top with different seeds, everything seasoning, cheese, etc.
Instructions To Make Fresh Milled Flour Bagels
- Firstly, mill the flour.
- Combine the flour, warm water, salt, and malt, mix until no dry flour is left. This should be a stiff dough.
- Cover and let sit at room temperature for at least 30 minutes or up to 2 hours.
- After the dough has sat, then add the yeast. Mix yeast in until incorporated.
- Knead the dough for at least 15 minutes. It will be very tough on a mixer, so if you want to knead by hand you can, or knead half with the mixer and half with your hands.
- Cover the dough again, and let it rise until it looks puffy. (We aren’t looking for it to double in size like bread, so it may only take 30-40 minutes.)

Shaping The Dough
- After the dough looks puffy, divide the dough into 8 pieces (the dough should be stiff enough that you don’t need oil or flour for your work surface.)
- Press each dough piece to get some of the air out, then roll each piece into an 8 inch cylinder. Make sure to keep all the other pieces covered that you are not working with so the dough pieces don’t dry out. Cover all the cylinders and let sit for 15 minutes.
- After this second rest, take each cylinder and wrap it around your hand with the ends of the dough under your hand. push the ends on the table in a rolling motion to “lock” the two ends together. Make sure the ends are securely sealed. (keep dough pieces covered when not working with them.)
- ALTERNATIVE SHAPING METHOD- rather than making the cylinders and wrapping around your hand, you could make a dough disk, and press two fingers in the middle of the dough all the way through. making the center hole larger than the two fingers.
- Place all shaped bagels on a parchment paper lined baking sheet, and cover securely with plastic wrap. Place the covered baking sheet in the fridge overnight. (6-24 hours)

The Next Morning
- The next morning it is time to get the water bath started.
- Pour the water, malt, and sugar into a large pot, and bring to a boil.
- If you are adding toppings, you would get those ready at this time.
- Preheat oven to 425*F.
- Once the water is boiling, carefully place the bagel dough into the boiling water. Don’t overcrowd your pot. Once you place the bagels into the boiling water, it will slow to a heavy simmer.
- Simmer the bagels for 40 seconds on one side, then flip them in the water. Simmer for 40 seconds on the other side. (I used a pair of tongs and gently flipped them.)
- Once boiled, if adding toppings, add them now while they are still wet.
- Then, when all bagels are done boiling, and on the lined baking sheet bake for 20-25 minutes, until they are a deep golden brown.

How To Store Fresh Milled Flour Bagels
To Store the fresh milled flour bagels, I recommend to slice and freeze them. They are wonderful the first day, and if unsliced they will keep for a couple days. But, if you let them cool completely, then slice them, and then freeze them in a freezer safe bag or container. Then, when you go to thaw them, they taste just like they were baked the same day!
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Bagels Made With Fresh Milled Flour Printable Recipe

NY Style Bagels made with Fresh Milled Flour
Ingredients
Bagel Dough
- 4 Cups fresh milled flour 480g I milled 400g of hard white wheat berries & 80g of Kamut berries to get this amount.
- 2 tsp salt
- 1 TBSP Malt syrup you could use molasses or brown sugar if needed instead
- 1&1/4 cup warm water 295g
- 1&1/2 tsp instant yeast
Water Bath Ingredients
- 2 quarts water 2000g
- 2 TBSP malt syrup you could use molasses or brown sugar if needed instead
- 1 TBSP sugar
Optional Toppings – you could top with different seeds, everything seasoning, cheese, etc.
Instructions
- Mill the flour.
- Combine the flour, warm water, salt, and malt, mix until no dry flour is left. This should be a stiff dough.
- Cover and let sit at room temperature for at least 30 minutes or up to 2 hours.
- After the dough has sat, then add the yeast. Mix yeast in until incorporated.
- Knead the dough for at least 15 minutes. It will be very tough on a mixer, so if you want to knead by hand you can, or knead half with the mixer and half with your hands.
- Cover the dough again, and let it rise until it looks puffy. (We aren’t looking for it to double in size like bread, so it may only take 30-40 minutes.)
- After the dough looks puffy, divide the dough into 8 pieces (the dough should be stiff enough that you don’t need oil or flour for your work surface.)
- Press each dough piece to get some of the air out, then roll each piece into an 8 inch cylinder. Make sure to keep all the other pieces covered that you are not working with so the dough pieces don’t dry out. Cover all the cylinders and let sit for 15 minutes.
- After this second rest, take each cylinder and wrap it around your hand with the ends of the dough under your hand. push the ends on the table in a rolling motion to “lock” the two ends together. Make sure the ends are securely sealed. (keep dough pieces covered when not working with them.)
- ALTERNATIVE SHAPING METHOD- rather than making the cylinders and wrapping around your hand, you could make a dough disk, and press two fingers in the middle of the dough all the way through. making the center hole larger than the two fingers.
- Place all shaped bagels on a parchment paper lined baking sheet, and cover securely with plastic wrap. Place the covered baking sheet in the fridge overnight. (6-24 hours)
The Next Morning
- The next morning it is time to get the water bath started.
- Pour the water, malt, and sugar into a large pot, and bring to a boil.
- If you are adding toppings, you would get those ready at this time.
- Preheat oven to 425*F.
- Once the water is boiling, carefully place the bagel dough into the boiling water. Don't overcrowd your pot. Once you place the bagels into the boiling water, it will slow to a heavy simmer.
- Simmer the bagels for 40 seconds on one side, then flip them in the water. Simmer for 40 seconds on the other side. (I used a pair of tongs and gently flipped them.)
- Once boiled, if adding toppings, add them now while they are still wet.
- Then, when all bagels are done boiling, and on the lined baking sheet bake for 20-25 minutes, until they are a deep golden brown.
Video
Notes
*This post contains affiliate links, which means I make a small commission at no extra cost to you! As an Amazon Associate I earn from qualifying purchases. But, I will only suggest items I actually Love and Have Used!
Does this need to get to windowpane?
No, this dough is too stiff to get to a window pane. Just knead until soft, smooth, and cohesive dough forms about 10 minutes. I recommend to checkout the video too! https://youtu.be/8bEgrRtkmcQ