Fresh Milled Sourdough Bagels
This post may contain affiliate links, which means we may receive a commission at no cost to you if you purchase through our links. As an Amazon Associate I earn from qualifying purchases.
I don’t know about you, but I love a good bagel. They’re simple yet delicious, and can be used in so many different ways. These fresh milled sourdough bagels are the perfect bread to keep on rotation in your from scratch kitchen.
When I can combine the health benefits of fresh milled flour and sourdough fermentation with a delicious bread like bagels, I’m one happy girl.
In our home we use bagels for all sorts of meals. From your average breakfast side to the perfect bread for lunch sandwiches, they can be a staple you fall back on again and again.
Not to mention, these fresh milled sourdough bagels are the perfect freezer prep bread (more on that in a bit). I just know you will love this recipe!
Why You Will Love These Fresh Milled Sourdough Bagels
Simple – On this blog we love simple, repeatable recipes and this bagel recipe is no exception. They use simple ingredients and don’t require much hands on time making them the perfect recipe for busy homes.
Healthy – Because of the fresh milled grains and the fermentation from sourdough, these bagels are just about as healthy as you can get! Nutrient dense, gut healthy and delicious… sign me up!
Delicious – Fresh milled flour has a natural taste that can only be described as something your body knows it needs. That paired with the gentle tang and depth from sourdough makes for one delicious bagel.

What is sourdough?
Sourdough is the process of natural leavening bread using a sourdough starter made from flour and water. The sourdough starter ferments the dough using wild yeast versus store-bought commercial yeast.
Rising your bread with a sourdough starter produces a lovely tangy taste and makes your bread not only delicious but gut-healthy as well. Because of the long fermentation and its ability to break down the grain, sourdough can make the bread easier to digest for those that are sensitive to gluten.
What is fresh milled flour?
Fresh milled flour is the flour you get by putting whole wheat berries (the part of wheat that makes flour) through a home grain mill. The flour you get out of your home grain mill differs greatly from store-bought flour for a few major reasons.
The first reason being, the fresh milled flour you get out of your mill is in its most whole, pure form. Unlike store-bought flour which is put through a commercialized milling process to optimize its texture and shelf-stability, fresh milled flour remains in its whole form with all of its original nutrient properties intact.
Because home milled flour is fresh, it contains the germ which can cause it to spoil quickly. The germ also contains much of the nutrition, but due to its perishable nature, it is removed in the commercial milling process, taking a bulk of the nutrition with it. Commercial flour is also often bleached and injected with synthetic vitamins and minerals to replace the naturally-derived versions that are lost when the germ is removed.
What is the best fresh milled flour for sourdough bagels?
My personal preference (what this recipe calls for) is to use a combination of 20% soft white wheat and 80% hard red or white wheat. While the soft white wheat is not completely necessary, it gives the bagels a soft, chewy texture that is absolutely delicious. You can use any type of hard wheat you would like for your fresh milled sourdough bagels.
Ingredients
Soft White Wheat
Hard Red or White Wheat
Filtered Water
Honey
Active Sourdough Starter
Salt
Baking soda
Tools You May Need
Mixer – Any mixer with a dough hook will work.
Grain Mill – I have the NutriMill Harvest and absolutely love it!
Bench Scraper
Food Scale – since this recipe is in grams, a food scale is needed
Large pot or dutch oven – I like using my dutch oven because it is nice and wide
Baking Sheet – I like these aluminum non-toxic baking sheets
Bread Making Tools

How to Make This Fresh Milled Sourdough Bagels Recipe
Step 1 – About 8-12 hours before you want to prepare your dough, feed 10 grams of sourdough starter with 70 filtered water and 80 grams flour (you can use all-purpose or fresh milled).
Step 2 – Once your starter is active and bubbly you can begin making the dough. Start by finely grinding the soft white wheat (100 g) and hard wheat (red or white is fine) (400 g) in your grain mill.
Step 3 – Combine the filtered water (250 g), active starter (150 g), honey (50 g), fresh milled flour, and salt (10 g) in the bowl of your stand mixer. Knead with your dough hook on a low speed for about 8-10 minutes. This dough will be very stiff and difficult to knead by hand, but if kneading by hand do so for at least 10-15 minutes.
Step 4 – Cover the dough and allow it to rise at room temperature until doubled, usually about 6-8 hours depending on the temperature of your kitchen. I like to mix up the dough at night so it is ready by morning, however you can refer to the sample schedules in this blog post to see what timeline might work best for you.
Step 5 – Once the dough is doubled, transfer it to the countertop and divide into 8 equal pieces. If you want to weigh them out for consistency, each piece should weigh about 110 g. Roll each piece into a ball and set aside. Allow the dough balls to rest for about 10 minutes.
Step 6 – Begin shaping the dough balls into bagels by placing your thumb directly into the middle of the dough ball. Then, using your fingers in the hole you just made, gently begin to stretch the ball out in a circular motion, creating a large hole in the middle. Repeat this process with all of the dough balls. Set them on a parchment lined baking sheet and cover with a damp tea towel. They will now complete their second rise, which usually takes about 1-2 hours.
Step 7 – When the bagels have risen, bring 6 quarts of water to a boil (I like to use my 8 qt dutch oven because it is nice and wide) and preheat your oven to 375ยฐF. Once the water is about boiling, add honey (2 tbsp) and baking soda (1 tbsp).
Step 8 – Now you will begin boiling the bagels by placing them into the pot of water. I can fit 4 at a time in my dutch oven, but if your pot isn’t as wide you may need to do less to avoid over crowding them. Boil them on one side for 2 minutes, then flip them oven and boil for 2 more minutes. Transfer bagels back to your parchment lined baking sheet.
Step 9 – If you are choosing to add toppings (see the “make these fresh milled flour sourdough bagels your own” section), do that at this point. Then bake your bagels at 375ยฐF for 25 minutes. If you are concerned whether they are done, check the internal temperature which should read at least 200ยฐF.
Step 10 – Serve your bagels for breakfast as a side or as the star for an egg sandwich, for lunch with deli meat or chicken salad or as a treat with flavored cream cheese. Enjoy!
For a visual, check out these step by step images!
Sample Sourdough Schedules
Sample Schedule #1
Day 1
8 PM – Feed sourdough starter per recipe instructions.
Day 2
8 AM – Knead together freshly milled flour, water, active starter, honey and salt in mixer. Cover and allow to rise for 6-8 hours.
2 PM – Divide dough and shape per recipe instructions. Cover and allow them to rise again.
4 PM – Prepare your water with honey and baking soda. Boil bagels per recipe instructions.
4:30 PM – Bake your bagels per recipe instructions and enjoy!
Sample Schedule #2
Day 1
12 PM – Feed sourdough starter per recipe instructions.
9 PM – Knead together freshly milled flour, water, active starter, honey and salt in mixer. Cover and allow to rise overnight.
Day 2
6 AM – Divide dough and shape per recipe instructions. Cover and allow them to rise again.
8 AM – Prepare your water with honey and baking soda. Boil bagels per recipe instructions.
8:30 AM – Bake your bagels per recipe instructions and enjoy!
Tips for making the best sourdough bagels with fresh milled flour
Substitutions
Soft white wheat – If you don’t have soft white wheat or prefer to use all hard wheat, you can all hard wheat
Honey – You can use sugar or maple syrup in place of honey in the dough recipe, but I recommend using honey in the water bath
Make these fresh milled flour sourdough bagels your own…
Add toppings to these fresh milled bagels to give them a fun twist, or leave them plain if you prefer!
Everything Bagel – Fill the bottom of a small bowl or plate with everything bagel seasoning. Press the boiled bagel into the seasoning top side down to coat it well.
Cheddar Cheese Bagel – Place shredded cheddar cheese (I highly recommend shredding your own cheese as pre-shredded cheese does not melt well) onto the tops of your bagels.
Cinnamon Sugar Bagel – Fill the bottom of a small bowl or plate with 1/2 cup sugar and 1 tsp cinnamon. Mix until the cinnamon and sugar are combined. Press the bagel into the cinnamon sugar top side down and coat well.
Fresh Milled Sourdough Bagels FAQ
Homemaker Tip
Double this fresh milled sourdough bagels recipe and slice all of the extra bagels in half. Store them in a ziplock bag in the freezer and pull them out to pop in the toaster for a quick breakfast, simple side or bread for a sandwich without ever dirtying up a dish!

Fresh Milled Sourdough Bagels
Equipment
- Mixer
- Grain Mill
- Large pot or dutch oven
- Baking sheet
Ingredients
Sourdough Starter
- 10 g sourdough starter
- 70 g filtered water
- 80 g flour fresh milled or all-purpose
Bagel Dough
- 100 g soft white wheat
- 400 g hard red or white wheat
- 250 g filtered water
- 150 g active sourdough starter
- 50 g honey
- 10 g salt
Water Bath
- 6 quarts water
- 2 tbsp honey
- 1 tbsp baking soda
Instructions
- About 8-12 hours before you want to prepare your dough, feed 10 grams of sourdough starter with 70 filtered water and 80 grams flour (you can use all-purpose or fresh milled).
- Once your starter is active and bubbly you can begin making the dough. Start by finely grinding the soft white wheat (100 g) and hard wheat (red or white is fine) (400 g) in your grain mill.
- Combine the filtered water (250 g), active starter (150 g), honey (50 g), fresh milled flour, and salt (10 g) in the bowl of your stand mixer. Knead with your dough hook on a low speed for about 8-10 minutes. This dough will be very stiff and difficult to knead by hand, but if kneading by hand do so for at least 10-15 minutes.
- Cover the dough and allow it to rise at room temperature until doubled, usually about 6-8 hours depending on the temperature of your kitchen. I like to mix up the dough at night so it is ready by morning, however you can refer to the sample schedules in this blog post to see what timeline might work best for you.
- Once the dough is doubled, transfer it to the countertop and divide into 8 equal pieces. If you want to weigh them out for consistency, each piece should weigh about 110 g. Roll each piece into a ball and set aside. Allow the dough balls to rest for about 10 minutes.
- Begin shaping the dough balls into bagels by placing your thumb directly into the middle of the dough ball. Then, using your fingers in the hole you just made, gently begin to stretch the ball out in a circular motion, creating a large hole in the middle. Repeat this process with all of the dough balls. Set them on a parchment lined baking sheet and cover with a damp tea towel. They will now complete their second rise, which usually takes about 1-2 hours.
- When the bagels have risen, bring 6 quarts of water to a boil (I like to use my 8 qt dutch oven because it is nice and wide) and preheat your oven to 375ยฐF. Once the water is about boiling, add honey (2 tbsp) and baking soda (1 tbsp).
- Now you will begin boiling the bagels by placing them into the pot of water. I can fit 4 at a time in my dutch oven, but if your pot isn't as wide you may need to do less to avoid over crowding them. Boil them on one side for 2 minutes, then flip them oven and boil for 2 more minutes. Transfer bagels back to your parchment lined baking sheet.
- If you are choosing to add toppings (see the "make these fresh milled flour sourdough bagels your own") section, do that at this point. Then bake your bagels at 375ยฐF for 25 minutes, If you are concerned whether they are done, check the internal temperature which should read at least 200ยฐF.
- Serve your bagels for breakfast as a side or as the star for an egg sandwich, for lunch with deli meat or chicken salad or as a treat with flavored cream cheese. Enjoy!
Notes
- Mill your grains finely in your mill for the best texture.
Did you make these fresh milled sourdough bagels?
If you tried this recipe, be sure to rate it and leave a comment below! Follow along with me on Pinterest for more delicious recipes, homemaking inspiration and more!





















