Fresh Milled Protein Bagels with Greek Yogurt
These fresh-milled protein bagels with greek yogurt are a flavorful and protein packed, but most importantly, they're made in under 1 hour! Traditional homemade bagels usually require yeast/sourdough, kneading, rising, and sometimes boiling before baking, but for this version, I only use baking powder for leavening, greek yogurt for protein, and freshly milled wheat for all the nutrition it offers.

Though it's a quick protein bagel recipe, they turn out soft, pleasantly chewy, and so good toasted with cream cheese, butter, or your favorite bagel toppings.
If you love making homemade bagels but don't mill your flour yet, try my quick greek yogurt protein bagels, or if you do mill flour but would like to try more traditional bagels, I also have fresh milled sourdough bagels recipe on my site.
Summarize & Adapt This Recipe On:
Quick Look
- Prep Time: 15 minutes
- Final Proof: 10 minutes
- Cook Time: 25-30 minutes
- Total Time: 50-55 minutes
- Servings: 4 bagels
- Difficulty: Easy
- Baking Method: Oven-baked
- Best For: Quick breakfasts, high-protein snacks, and homemade bagel sandwiches
Jump to:
- Summarize & Adapt This Recipe On:
- Quick Look
- Important Ingredients
- Substitutions & Variations
- How to Make Fresh Milled Protein Bagels with Greek Yogurt
- Baking Schedule
- 💭Crucial Success Tips
- Recipe FAQs
- How To Store Fresh Milled Protein Bagels with Greek Yogurt
- Other Delicious Fresh Milled Bread Recipes
- Fresh Milled Protein Bagels with Greek Yogurt
- Need Help Tweaking This Recipe?
- Other Fresh Milled Flour Recipes You'll Love
- Fresh Milled Einkorn Banana Bread
- The Easiest Fresh Milled Einkorn Sourdough Bread (Loaf Pan Method)
- Fresh Milled Einkorn Kaiserschmarrn (Shredded Pancake)
Important Ingredients
- freshly milled hard white wheat flour provides whole-grain flavor and a pleasantly chewy texture. Mill on a fine setting for softer bagels.
- full-fat greek yogurt adds protein, moisture, and tenderness to the dough. Low-fat Greek yogurt works too.
- baking powder helps the bagels rise without needing yeast or a long fermentation time.
- salt enhances the flavor of the freshly milled flour.
- egg used for brushing the tops to create a golden-brown finish and help toppings stick.
See recipe card for quantities.
Substitutions & Variations
- Hard red wheat can be used instead. It has a slightly stronger flavor, but I honetly prefer it (my kids do not though).
- You can use low-fat plain Greek yogurt works too. Use thick Greek yogurt rather than regular yogurt for the right dough consistency.
- Make sure your baking powder is fresh so the bagels rise properly.
- You can skip the egg wash, although the tops may not become as golden.
How to Make Fresh Milled Protein Bagels with Greek Yogurt

Step 1: Whisk together the freshly milled flour, baking powder, and salt. Add the Greek yogurt and mix just until a soft dough forms (Image 1). Don't knead it, mix it just until it's incorporated.

Step 2: Divide the dough into four equal portions. Shape each one into a ball, make a hole in the middle (Image 2), and place it on the prepared baking sheet. The dough will be sticky and not very easy to shape, so use wet hands and work quickly. The dough will get stickier the longer you're trying to shape it, so work fast and don't overwork it.

Step 3: Let the shaped bagels rest for 10 minutes (Image 3). This gives the freshly milled flour a little time to absorb the moisture and the baking powder to begin doing its job without making the dough harder to shape.

Step 4: Brush the bagels with beaten egg and add your chosen toppings (Image 4) and bake for 25-30 minutes at 190°C (375°F), until puffed and golden brown. Let them cool for at least 20 minutes before slicing.
Hint: Use full-fat Greek yogurt. It adds a creamy flavor and moisture to the dough, although low-fat Greek yogurt works too.
Baking Schedule
- 8:00 AM - preheat oven and prepare baking sheet
- 8:05 AM - mix the ingredients
- 8:10 AM - divide dough and shape bagels
- 8:15 AM - rest the bagels
- 8:25 AM - brush with egg wash and add toppings
- 8:30 AM - bake
- 9:00 AM - remove from oven and cool
- 9:20 AM - slice, toast, and enjoy!
💭Crucial Success Tips
Use freshly milled flour on a fine setting (as fine as you can go, to hear the stones clinking together on stone mills). This helps create a softer, more pleasant texture in the finished bagels.

Recipe FAQs
Yes! Hard red wheat works as a substitute for hard white wheat. It has a slightly stronger, nuttier flavor, while hard white wheat generally produces a milder-tasting bagel.
Yes! You can bake them ahead and store them for quick breakfasts throughout the week. They're especially good toasted the next morning with cream cheese, butter, or your favorite sandwich fillings.
This dough is naturally sticky because of the Greek yogurt and freshly milled flour. Use wet hands when shaping, work quickly, and avoid adding extra flour unless the dough is unusually wet and difficult to handle.
How To Store Fresh Milled Protein Bagels with Greek Yogurt
Once completely cooled, store the bagels in an airtight container or bread bag for up to 2 days. Keep them in a cool, dry spot.
In the Refrigerator: Store cooled bagels in an airtight container for up to 5 days.
In the Freezer: Slice the completely cooled bagels in half and place them in a freezer-safe bag. Freeze for up to 2 months.

Other Delicious Fresh Milled Bread Recipes
- Fresh Milled Protein Bagels with Greek Yogurt
- Fresh Milled Pumpkin Sourdough Rolls with Poppy Seed Filling
- Einkorn Sourdough Bread for Beginners (50% Fresh Milled)
- The Easiest Fresh Milled Einkorn Sourdough Bread (Loaf Pan Method)
If you tried these fresh milled protein bagels with greek yogurt or any other recipe on my blog please leave a 🌟 star rating and let me know how it went in the 📝 comments below! Happy Baking!

Fresh Milled Protein Bagels with Greek Yogurt
Ingredients
- 130 grams freshly milled hard white wheat flour
- 6 grams baking powder about 1½ teaspoons
- 2-3 grams salt ¼ to ½ teaspoon
- 230 grams full-fat plain Greek yogurt low fat works too, I just prefer full fat for the taste
- 1 large egg beaten, for brushing
- Optional toppings: sesame seeds or everything bagel seasoning
Instructions
- Whisk together the freshly milled flour, baking powder, and salt. Add the Greek yogurt and mix just until a soft dough forms. Don't knead it, mix it just until it's incorporated.
- Divide the dough into four equal portions. Shape each one into a ball, make a hole in the middle, and place it on the prepared baking sheet. The dough will be sticky and not very easy to shape, so use wet hands and work quickly. The dough will get stickier the longer you're trying to shape it, so work fast and don't overwork it.
- Let the shaped bagels rest for 10 minutes. This gives the freshly milled flour a little time to absorb the moisture and the baking powder to begin doing its job without making the dough harder to shape.
- Brush the bagels with beaten egg and add your chosen toppings and bake for 25-30 minutes at 190°C (375°F), until puffed and golden brown. Let them cool for at least 20 minutes before slicing.
Notes
- You DON'T need to shape this into bagels! You can do cute little rolls, but I find that making a hole in the middle is just very practical: it bakes better and it's just more pretty (in my opinion). If you do end up making rolls, make sure to add a few minutes to your baking time!
- Mill the hard white wheat on a fine setting for the softest texture.
- Shape the bagels immediately after mixing, then let them rest on the baking sheet.
- Don't add extra flour just because the dough feels sticky. Wet hands make it much easier to handle.
- These are softer than traditional yeast-leavened bagels, but the hard white wheat still gives them a pleasantly chewy texture.
- You can use hard red wheat instead of hard white








