These freshly milled sourdough bagels are crunchy on the outside and chewy on the inside. Make these with your sourdough starter for a delicious breakfast or lunch. We like to freeze them too and pull them out to toast another time. Learn how to make homemade freshly milled sourdough bagels with this easy tutorial.

These freshly milled sourdough bagels are crunchy on the outside and chewy on the inside. Make these with your sourdough starter for a delicious breakfast or lunch. We like to freeze them too and pull them out to toast another time. Learn how to make homemade freshly milled sourdough bagels with this easy tutorial.
A Delicious and Nutritious Summertime Lunch
As we approach summer and picnic season, I am looking for easy recipes to reach for that are good for on the go. These freshly milled sourdough bagels are just that. And, super delicious with loads of nutrition in each bite.
I first started making sourdough bagels several years ago and my family totally loved them. Considering how delicious bagels are from the store, I was a little nervous to try to replicate those.
But honestly after years of making these and not buying store-bought bagels, I really changed my mind about that. And my husband too even! So, homemade bagels are absolutely worth making my opinion.
Now that we have a grain mill I have been repurposing my recipes to accommodate freshly milled grain. It’s the best! These freshly milled sourdough bagels are the perfect lunch recipes to use your freshly milled flour.
I hope your family loves them as much as mine!
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How are freshly milled grains healthier for you?
Freshly milled grain is healthier for you because it keeps the entire grain intact, including the bran, germ, and endosperm. Today, most store-bought flour has stripped away the bran and germ and all of their nutrients in order to maintain a longer shelf life.
That means you’re getting more fiber, B vitamins, healthy fats, and antioxidants in every bite, which can support digestion, heart health, and stable blood sugar. Yes please!
And if you think about it, whole grain is also the original form of wheat that God gave us from the beginning. I don’t know about you, but I am always thinking about how we can enjoy the original Earth God created and use it to nourish our bodies, which can be hard in today’s world of modern advances and technologies. But I believe God created grain to be eaten in its whole form, and that our bodies actually thrive when eaten this way!
This is why many people today are tolerating whole grains that are freshly milled, or even ancient grains like Einkorn, much better than the highly processed white all purpose flour we see sold at stores today.
If you’re looking for a place to source whole wheat berries, we get ours from Azure Standard! We buy in bulk so I only have to pick it up every few months. And, I love trying the many wheat varieties.

What is sourdough starter?
Making sourdough is the process of fermenting the flour grain with water over time. This process creates those healthy live cultures and allows the good bacteria to overcome the grain. When this happens, the phytic acid is striped away from the grain, which minimizes the gluten content.
This is why many people prefer to eat sourdough or better yet keep their own sourdough starter, so they can enjoy bread products that taste better and are healthier for your too. Source
We started making sourdough starter when we realized how easy it was, how much healthier it is for you, and how much better it tastes! Learn how to make a sourdough starter here. And yes, you can use your freshly milled flour for that too!

Benefits of Sourdough
When you feed your starter with flour and water, the live cultures are feeding off the sugar in the gluten. As they do this, something called phytic acid is being reduced. This is the acid that exists on non-fermented grains that can make grain difficult to digest.
This goes for all fermented foods like fermented milk kefir, soaked oats, sauerkraut, etc.
New to Sourdough?
You can learn how to make your own sourdough starter from scratch to make homemade bread, sourdough pizza, bagels, and more.
Put all your sourdough recipes in one spot!
Download and print off this NEW sourdough recipes ebook and keep your favorite sourdough recipes on your counter for easy, every day cooking.





More From Scratch Breakfasts from the Homestead
Freshly Milled Sourdough Buttermilk Pancakes
Einkorn Sourdough Raspberry Pop Tarts
Make-Ahead Cast Iron Skillet Breakfast
Tools Needed
Mixing Bowl (you could also use a stand up mixer with dough attachment)
Baking Tray lined with parchment paper
Tongs
Fork
Freshly Milled Sourdough Bagel Ingredients
3/4 cup sourdough starter
1 1/4 cup filtered water
2 tsp salt
3-4 tbsp honey
1 tbsp avocado oil
2 cups hard white wheat berries (about 2 1/2 cups of freshly milled flour)
1 1/2 cups all purpose flour
Example Freshly Milled Sourdough Bagel Timeline
If you want bagels for Sunday morning brunch at 11am:
Saturday 9am: take sourdough starter out of refrigerator. Feed it 1 cup flour and 3/4 cup water. Cover and let sit on the counter or in an oven with a “proof” setting.
Saturday after 3pm: Check the starter. It should be bubbly and active. Try putting a spoonful in water and seeing if it floats. If it floats, it’s ready. Go ahead and make the bagel dough.
Saturday night: bagel dough sits out on the counter overnight.
Sunday 9am: punch bagel dough down and form into bagels. Cover and lit sit 1 hour.
Sunday 10am: boil the water and bake the bagels.
How to Make Sourdough Bagels Step by Step
Note: feed your sourdough starter at least 6 hours before starting this, and let it sit until it is bubbly and active. If you are new to sourdough starter, get started here. If you are trying to make bagels for breakfast, you’ll want to make the dough per the instructions below the day before.
The Night Before: Make the Dough
In a large mixing bowl or a stand up mixer with dough attachment, combine the sourdough starter, water, salt, olive oil, and honey. Use a fork to whisk together until combined.

Then add the freshly milled flour and kneed until a stretchy, sticky dough is formed. You can use a stand up mixer with dough hook or your hands. It will take a few minutes either way. Loosely cover the bowl with plastic wrap and let sit out on your counter overnight. Make sure the dough has enough room to grow!
Let the dough sit on the countertop overnight. You do not need to do stretch and folds like you would for making bread, but you can if you want extra fluffy bagels.

The morning of: Make the Bagels
The next morning, divide the dough into 6 parts, cutting it down the middle with a knife or dough cutter and then cutting each half into 3 triangles.

Form the bagels by rolling the triangles into a ball in your hands, then using a finger to create the hole in the center.

Place the bagels on a parchment lined baking sheet. Cover with a tea towel or plastic and let sit about 1-2 hours, or until doubled in size.

How to Make Bagels, Cont.
Preheat the oven to 425 degrees F.
Bring a large pot of water to boil on the stove. Add the sugar to the water. Meanwhile add the bagel seasoning or shredded cheese topping to a plate and set aside.
Add the bagels to the boiling water and boil 1 minute each side. Use tongs to flip. Only add a few bagels at a time, making sure not to overcrowd the water. Keep in mind the bagels will grow in the water.

Shake the water off the bagels and place them on a parchment lined baking tray. Then add your toppings. We like shredded cheese or the everything bagel seasoning.

Once all the bagels are on the baking sheet, bake them for 20 minutes.
Remove from the oven and let sit 10 minutes before serving. Tip: whatever bagels you don’t eat that day, cut them in half and store them in the freezer. They make great leftovers!
Add cream cheese, salmon lox, or meat cuts for a lunch option. The opportunities are endless!
You can either dip the bagel in seasoning/cheese, or you can place it on the baking tray and drizzling the topping right on top. Either way works great!

Tips for Making Sourdough Bagels
Everyone has different sourdough starters. Depending on where you live, the quality of your water and air, and the type of flour you’re using will vary the results of your sourdough products. So the best thing to do is learn what good sourdough “dough” looks like.
Your dough should be sticky to the touch but not so sticky that it doesn’t form a ball. It should come together in a ball easily, but if you have dough all over your hands it’s too sticky. But if you have no dough on your hands it’s probably too dry. Adjust the flour and water accordingly to get the dough that’s just right. If it’s way too sticky, add flour. If it’s too dry, add water.
Your dough will grow overnight quite a bit! Make sure you have it in a large bowl so it has space, and don’t put the plastic on too tightly.
Start the recipe the day before you want the bagels. If that’s too much planning for you (or you’re tired of wanting bagels but never having them at the right time), I suggest making these bagels one day and freezing them for later. They freeze really well and taste just as good! Just make sure you cut them in half before freezing.
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FAQs:
Are freshly milled sourdough bagels healthy?
Freshly milled sourdough bagels made with sourdough starter will be long fermented, and therefore have the benefits of fermented grain.
They will also have the health benefits of freshly milled flour, which includes the bran and germ of the whole grain. This means the bagels will be higher in vitamins, minerals, and nutrients, making them a much healthier meal option than a typical store-bought bagel.
Why are my sourdough bagels flat?
It could be that your sourdough starter wasn’t strong enough to make the bagels rise. Try the “float test” next time. Feed your starter with 1 cup flour and 3/4 cup water and let it sit at least 6 hours. The starter is ready for baking when a spoonful of it floats in a cup of water.
How do you store sourdough bagels?
Wrap them in plastic and store at room temp or in the fridge for up to 3 days. My favorite way to store them though is to freeze them. Just slice them in half and store in a freezer bag. Then just pop them in the toaster or on a cast iron to heat them back up.

More Delicious Sourdough Recipes

Freshly Milled Sourdough Bagels
Learn how to make freshly milled sourdough bagels that are crunchy on the outside and chewy on the inside. These homemade bagels are nutrient dense and gut healthy, making them a delicious and nutritious lunch any time of year.
Ingredients
- 3/4 cup sourdough starter
- 1 1/4 cup filtered water
- 2 tsp salt
- 3-4 tbsp honey
- 1 tbsp avocado oil
- 2 cups hard white wheat berries (about 2 1/2 cups of freshly milled flour)
- 1 1/2 cups all purpose flour
Instructions
The Night Before: Make the Dough
In a large mixing bowl or a stand up mixer with dough attachment, combine the sourdough starter, water, salt, olive oil, and honey. Use a fork to whisk together until combined.
Then add the freshly milled flour and kneed until a stretchy, sticky dough is formed. You can use a stand up mixer with dough hook or your hands. It will take a few minutes either way. Loosely cover the bowl with plastic wrap and let sit out on your counter overnight. Make sure the dough has enough room to grow!
Let the dough sit on the countertop overnight. You do not need to do stretch and folds like you would for making bread, but you can if you want extra fluffy bagels.
The Morning Of: Make the Bagels
The next morning, divide the dough into 6 parts, cutting it down the middle with a knife and then cutting each half into 3 triangles. Form the bagels by rolling the triangles into a ball in your hands, then using a finger to create the hole in the center. Place the bagels on a parchment lined baking sheet. Cover with a tea towel or plastic and let sit 1-2 hours, or until doubled in size.
Preheat the oven to 425 degrees F and line a baking tray with parchment paper.
Bring a large pot of water to boil on the stove. Add the sugar to the water. Meanwhile add the bagel seasoning or shredded cheese topping to a plate and set aside.
Add the bagels to the boiling water and boil 1 minute each side. Use tongs to flip. Only add a few bagels at a time, making sure not to overcrowd the water. Keep in mind the bagels will grow in the water.
Shake the water off the bagels and place them on a parchment lined baking tray. Then add your toppings. We like shredded cheese or the everything bagel seasoning.
Bake the bagels for 20 minutes or until just browned on top.
Remove from the oven and let sit 10 minutes before serving. Tip: whatever bagels you don't eat that day, cut them in half and store them in the freezer. They make great leftovers!
Add cream cheese, salmon lox, or meat cuts for a lunch option. The opportunities are endless!
Notes
Feed your sourdough starter at least 6 hour before starting this, and let it sit until it is bubbly and active. If you are new to sourdough starter, get started here.
You may need more or less flour depending on the type of flour you're using and the consistency of your starter. If your dough is runny, add more flour. If the dough is too dry and not coming together, add more water.
Nutrition Information:
Yield: 6 Serving Size: 1Amount Per Serving: Calories: 415Total Fat: 3gSaturated Fat: 0gTrans Fat: 0gUnsaturated Fat: 3gCholesterol: 0mgSodium: 782mgCarbohydrates: 90gFiber: 6gSugar: 35gProtein: 10g
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