Pumpkin Sourdough Bagels with Cinnamon‑Swirl & Fresh-Milled Flour

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BySarah | Grains & Greens Kitchen Posted on
Cinnamon‑Swirled Pumpkin Sourdough Bagels
— Cinnamon Roll Meets Whole Grain Bagel

Soft, chewy sourdough bagels made with homemade pumpkin purée, fresh-milled whole grain flour, and a cozy swirl of brown sugar and cinnamon — simple, elegant, nourishing.

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Whole grain fresh-milled pumpkin sourdough bagels served in a basket lined with an embroidered linen cloth. One bagel is split to expose the dark brown cinnamon sugar swirl.
Whole grain fresh-milled pumpkin sourdough bagels served in a basket lined with an embroidered linen cloth. One bagel is split to expose the dark brown cinnamon sugar swirl.

I first fell in love with American baking in high school. There was a small coffee shop across the street, serving specialty roasts to mostly unenlightened students (who really just cared about the syrup shot in their lattes).

But the secret attraction was the pastries. Every morning, there was a fresh delivery, straight from an America bakery in the heart of Berlin, serving classic U.S. treats. (Barcomi’s, if you’re in Berlin and curious.)

There was a display case with all kinds of bagels, and every time I entered the shop, I quickly scanned for one thing and one thing only: cinnamon raisin bagels.

They were bronzed and golden, and if you had the time, split, toasted, and slathered in melting butter was the way to go. Most days, when I went for a cup of coffee, I’d leave with a little white paper bag holding a fresh cinnamon raisin bagel.

Why You’ll Love This Whole Grain Sourdough Bagel Recipe

The coffee shop across my old school is still there. But these days, I’s rather bake at home with fresh-milled flour than take a trip on a crowded train just to buy a white flour bagel.

For years, I’ve been revisiting cinnamon bagels every once in a while, but I never pulled anything from the oven that matched my initial bagel obsession — until now.

Every recipe I tried before either diluted the cinnamon into the dough, or mixed it in unevenly. Nothing delivered the intense pockets of cinnamon-coziness I was craving. That’s when I realized that what I really wanted, was the coziness of a cinnamon roll, but in breakfast format. That’s how these bagels were born. They’re the love child of two iconic pastries, a cross between cinnamon rolls and whole grain bagels.

These bagels check all the boxes for me. They’re soft and chewy in the middle, with that toothsome crust on the outside. The cinnamon swirl is buttery and brown sugar-cozy. They’re just as good plain as they are toasted, with those cinnamon layers crisped to perfection. Best of all, they leave me feeling full and energized — not weighed down.

And if those aren’t the boxes that you need checked in a cinnamon and pumpkin sourdough bagel, here are some more reasons to love this fresh-milled (or whole grain) recipe:

  • Soft & Chewy Sourdough Bagels — Even with whole grain (or fresh-milled) flour, these bagels have all the classic chew and tenderness of a traditional bagel.
  • Naturally Leavened with Sourdough Starter— Long fermentation adds flavor and supports easier digestion. (In a hurry? There’s an option for sourdough discard and instant yeast, too.)
  • Pumpkin & Cinnamon Flavor — Cozy and fall-festive, with real pumpkin puree and a buttery brown sugar cinnamon swirl.
  • Easy Yet Impressive — The cinnamon roll-style swirl looks bakery-worthy but is simple to make at home.
  • Make-Ahead Breakfast — Bake once, freeze for later. They toast beautifully from frozen and taste freshly made.
  • Perfect for Brunch or Holiday Guests— Toast straight from the freezer for a warm, comforting breakfast with zero stress.
  • Ancient Grain Bagel — Uses fresh-milled spelt (or soft wheat) for more flavor and nutrition.
  • Vegan Cinnamon Bagel Option — Just use vegan butter to make them dairy-free, and maple syrup to make them 100% plant-based.

Why Fresh-Milled Spelt Pumpkin Bagels?

Spelt is an ancient grain, related to modern wheat but with less gluten and a more fragile gluten structure. Because of that, it’s often deemed easier to digest. Personally, I love it for its complex, nutty yet soft flavor and tender texture. For the most intense flavor, I love using fresh-milled flour, which also preserves more nutrients when milled right before baking. Call me biased—but I can actually feel the difference.

However, spelt bread naturally tends to dry out more quickly. Even enriched breads won’t retain moisture as well as wheat bread. In Germany, bakers often use a scald called Mehlkochstück (similar to the Chinese tangzhong method) to lock in moisture for spelt loaves.

But there’s an easier way to get a tender, moist whole grain spelt crumb—pumpkin puree!
It’s quicker than a scald, makes a tender, chewy crumb, and adds a lovely, orange color to your bagels.

It’s the easiest baking hack to give whole grain bread that familiar chew and softness we love in modern refined wheat bread. You get all the cozy comfort of a classic breakfast with a fall twist—plus better nutrition and more stable blood sugar.

And, if ancient grains aren’t your thing or you prefer to keep your kitchen minimal, fresh-milled soft wheat is a perfect substitute with no recipe changes needed.

Tools You May Need

One fresh-milled pumpkin sourdough bagel, sitting on a light blue late, next to a pile of bright orange pumpkins. The orange hued whole grain bagel is split in the middle, to expose the dark brown cinnamon sugar swirl filling.
One fresh-milled pumpkin sourdough bagel, sitting on a light blue late, next to a pile of bright orange pumpkins. The orange hued whole grain bagel is split in the middle, to expose the dark brown cinnamon sugar swirl filling.

Stand Mixer (Optional): You can also knead by hand, of course.

Rolling Pin: For rolling out the dough into an even rectangle.

Large Pot: For boiling the bagels before baking.

Slotted Spoon: For carefully lifting the cooked bagels out of the hot water.

Ingredients and Substitutions

Whole Grain Spelt Flour If you can, use fresh-milled flour for best flavor (and nutrition). If you’re not milling at home (yet), store-bought whole grain spelt flour will work as well. You can skip the initial 30-minute rest with store-bought flour if you’re pressed for time.
If you’re not into ancient grains, fresh-milled soft wheat is a perfect stand-in.

Sourdough Starter Use active and bubbly starter that’s been fed within the last 4-8 hours. If your starter lives in the fridge, you can use it cold as long as it’s been fed within the past week.
Want to learn more about keeping a starter in the fridge? Check out my post on Maintaining a Sourdough Starter.

Pumpkin Puree I always use homemade pumpkin puree (partly because it tastes better, but mostly because canned pumpkin isn’t available in Germany). Canned pumpkin is usually drier than homemade, so if your dough feels very dry, feel free to add another tablespoon of water.

Brown Sugar: I use a lighter German brown sugar for the cinnamon swirl filling. You can use raw cane sugar, dark brown sugar, or any kind of muscovado or any whole raw cane sugar instead.

Butter: Use a high-quality vegan block butter if you want to make these bagels dairy-free.

Baking Soda: This is for the boiling water, not the dough. It’s won’t turn these bagels into pretzels, but gives them a pleasantly chewy, toothsome crust.

How to Make Cinnamon-Swirled Pumpkin Spelt Bagels (Step-by-Step)

01

Mix and rest the Dough

To the bowl of a stand mixer add water, pumpkin puree, sourdough starter, honey and salt.

Weigh out whole spelt berries and grind them on the finest setting of your grain mill. You can mill the flour right into the bowl with the wet ingredients.

Use the paddle attachment to mix the dry and wet ingredients until there are no dry bits of flour on the bottom of the bowl. Cover and rest for 30 minutes to properly hydrate the flour.

All wet ingredients for pumpkin sourdough bagels combined in a stainless steel bowl.
Shaggy cinnamon pumpkin sourdough bagel dough in the bowl of a stand mixer, ready for resting.

02

Knead the Dough

Switch to the dough hook and knead the dough for 7 minutes on the lowest speed. It should come together into a smooth, firm but pliable ball. Cover and bulk ferment for 6-8 hours, until the dough is puffy and about doubled in size.
(Fermentation time may vary, depending on the strength of your starter and the temperature of your kitchen.)

A beautiful orange hued pumpkin sourdough bagel dough in the stainless steel bowl of a stand mixer, being kneaded with the dough hook.
Risen and puffed whole grain sourdough bagel dough sitting in a stainless steel bowl.

03

Roll Out and Shape Bagels

When the dough has doubled in size, stir together melted butter, sugar and cinnamon. It should be thick and spreadable.

(You can chill the mix in the fridge while you roll out the dough, if it’s still too wet and soupy.)

Melted butter, brown sugar and cinnamon, added on top of each other in a hand glazed clay bowl.
Cinnamon swirl ingredients mixed in a white bowl with lightly turquoise rim. The surface is dark and shiny.
Thickened cinnamon swirl filling sittinin in a white and blue bowl, next to the rolled out, orange hued pumpkin sourdough bagel dough.

Lightly flour your worktop and the top of the dough with flour. Roll the dough out into as neat a rectangle as you can. Don’t roll it out too thin, or the layers might rip during shaping.

Spread the cinnamon filling evenly across the dough. Divide the dough into four equal parts, then cut each new rectangle into two triangles. Roll up each triangle from the tip towards the long side.

Orange hued pumpkin sourdough bagel dough, rolled out o a wooden kitchen counter, spread evenly with a dark brown and shiny cinnamon brown sugar filling. the dough is cut into triangles.
Orange hued pumpkin sourdough bagel dough, rolled out o a wooden kitchen counter, spread evenly with a dark brown and shiny cinnamon brown sugar filling. the dough is cut into triangles and the first triangle is halfway rolled up from the short side.

Take the rolled up piece of dough into your hands and gently press down from the middle out towards the end, to create a longer rope. Wrap the dough around your fingers and gently press the ends together until sealed.

Two hands gently holding a rolled up piece of cinnamon-swirled pumpkin sourdough bagel dough, ready to shape it into a rope.
Two hands gently pressing a rolled up piece of cinnamon-swirled pumpkin sourdough bagel dough out into a rope.
A cinnamon-swirled rope of sourdough pumpkin bagel dough rapped around three fingers of one hand, showing how to pinch together the ends to form a round bagel.

Place the shaped bagels onto a baking sheet lined with baking paper. Cover with plastic wrap and let them rise for 1-2 hours, or until the bagels are puffy but not doubled again.

Shaped cinnamon-swirled pumpkin sourdough bagels proofing on a parchment paper lined baking tray, next to a patterned tea towel.
Shaped cinnamon-swirled pumpkin sourdough bagels proofing on a parchment paper lined baking tray, next to a patterned tea towel.

04

Boil and Bake Bagels

Preheat the oven to 210°C (410°F).

In a large pot, bring 2 litres (8 cups) of water to a boil. Add 1 tablespoon sugar and 1 tablespoon baking soda (and enjoy the cauldron bubble). Turn the heat down to a simmer. Gently lower two bagels at a time into the simmering water and boil for 1 minute. Flip once and boil the other side for another minute.

A proofed and puffy raw pumpkin sourdough bagel is being boiled in a cast iron pot, bottom side up, next to the baking tray.
Two proofed and puffy raw pumpkin sourdough bagels being boiled in a cast iron pot, right side up. The crust is firming up and already turning orange.

Carefully lift out the boiled bagels with a slotted spoon and place them back on the baking sheet. Once all bagels are boiled, bake for 20-25 minutes, or until the bagels turn golden brown.

Place the sheet on a cooling rack and let the bagels cool down.

Golden brown fresh-milled cinnamon-swirled pumpkin sourdough bagels, baked to perfection, resting on a parchment lined baking tray. The perfect combination of cinnamon-roll and whole grain bagel!
Golden brown fresh-milled cinnamon-swirled pumpkin sourdough bagels, baked to perfection, resting on a parchment lined baking tray. The perfect combination of cinnamon-roll and whole grain bagel!

A Word about Handling Ancient Grains

Handle With Care.

Here are a few things to keep in mind when working with lower-gluten ancient grains:

  • Don’t Roll Too Thin: The dough triangles will need to be rolled up, stretched into ropes and shaped into rounds. If you roll the dough too thin, the layers might tear during shaping or boiling.
  • Press, Don’t Pull: Use a light hand when shaping the bagels. Instead of pulling the dough to stretch it, hold it in both hands and gently press outward from the center to elongate into a rope.
  • Go Slow: If the dough resists stretching, pause and just hold it as is for 10-15 seconds, until you feel it relax.
  • Pinch To Seal: Don’t roll the ends of the rope together. Instead, gently press them together for 15–20 seconds to seal. It’s less stressful on the dough but more than enough to keep them from unravelling during boiling or baking.
A hand holding a cut pumpkin sourdough bagel, spread with a generous lick of cream cheese.
A hand holding a cut pumpkin sourdough bagel, spread with a generous lick of cream cheese.

Additional Tips

  • Don’t Add More Water: It might be tempting but bagel dough is stiffer by design. The kneaded dough should be firm but pliable. There will be additional moisture from the butter in the filling and from boiling, of course. If you add too much water, shaping will be that much harder (and the proofed bagels will probably stick to the parchment paper).
  • Melt and Cool Butter: The cinnamon sugar filling should be thick and spreadable, not wet and soupy. If the filling is too loose, let it cool down and firm up before using. You can also place it in the fridge for 5-10 minutes if necessary.
  • Tears Are Part Of Life: Don’t worry if the shaped bagels should tear here and there after all. They’ll survive the water bath just fine. If anything, slightly exposed cinnamon swirls will turn extra crispy and caramelized in the oven.
  • Boil Upside Down: When lowering the proofed bagels into the boiling water, make sure the bottom side is up first. That way they’ll be right side up when they finish boiling and it’s a lot easier to slide them off the slotted spoon and back on the parchment paper.
  • Bake a Little Lighter: If you plan to freeze these bagels for later, pull them out of the oven earlier. They should be set and starting to brown but still a little soft to the touch. That way they come out perfectly crisp but not burnt from the toaster.

Variations

Let your pantry (and your cravings) guide you.

  • Need It Quicker? If you’re short on time, you can use sourdough discard from the fridge and add 1 sachet (7g) of instant yeast. Let the dough rise for 1 hour before shaping, then rise for about 30 minutes before boiling.
  • Add Raisins: I first fell in love with cinnamon raisin bagels — so feel free to add a cup of raisins! Soak them in hot water or black tea (or something stronger, if you like) first.
  • Try a Topping: Add toppings after boiling for extra flavor or texture. Pearl sugar, pumpkin seeds, poppy seeds, or a sprinkle of cinnamon sugar all pair beautifully.
  • Swap the Spice: For an even cozier fall flavor, replace the cinnamon with pumpkin pie spice.
Overhead shot of a split and toasted cinnamon-swirled pumpkin sourdough bagel made with fresh milled flour. One half is spread with butter, the other one shows the gorgeous cinnamon swirl. A basket full of bagels and some pumpkins are visible next to the light blue plate.
Overhead shot of a split and toasted cinnamon-swirled pumpkin sourdough bagel made with fresh milled flour. One half is spread with butter, the other one shows the gorgeous cinnamon swirl. A basket full of bagels and some pumpkins are visible next to the light blue plate.

How to Serve Sourdough Pumpkin Cinnamon Bagels

These bagels toast like a dream! They get crispy on the edges and the cinnamon sugar swirls get extra caramelized.

My favorite way to eat a cinnamon pumpkin bagel is to toast it until bronzed and crispy in a toaster or contact grill. Spread butter and watch it melt into the toasted swirls.

For a more indulgent Sunday spread, serve with cream cheese and honey, brie or cheddar. A side of bacon and eggs will make it worthy of any holiday brunch or breakfast.

How to Store and Freeze Spelt Sourdough Pumpkin Cinnamon Bagels

At Room Temperature:
Bagels keep well, wrapped, for up to 2 days before drying out. They last for up to 4 days, but I recommend freezing any leftovers after day 2 (instructions below).

In The Freezer:
Amazingly, these bagels are even better out of the freezer.

If you have any leftovers on day 2, split sourdough bagels and separate both halves with a piece of parchment paper. Place in a freezer bag and press out as much air as possible.

You can toast them straight from frozen and they come out better than new! The moisture will redistribute while the edges turn crispy and caramelize. Ideal if you’re hosting over the holidays.

Recipe FAQs

Yes! If you forgot to feed your starter in time, have some discard on hand, or just want to bake on a whim, you can replace the active starter with sourdough discard and add 1 sachet (7g) of instant yeast to the dough. Let the kneaded dough rest for 45-60 minutes, then shape and fill your bagels. After shaping, let them proof for 30 minutes before boiling.

Yes, of course! Store-bought whole grain spelt flour can be used in place of fresh-milled spelt flour. Alternatively, If you’re baking in Europe or anywhere else in the world where “hard wheat” isn’t common (and can only be found listed on a bag of pasta), you can substitute with whole wheat flour. In North America, where whole wheat flour is typically made from hard wheat, you might want to try white whole wheat flour. It’s the closest match to soft wheat whole wheat flour, though it will still behave a little differently.

Stay calm. it’s not the end of the world. As long as the ends are sealed, they’ll be fine. I have tested these extensively and even when the dough ripped to expose the cinnamon swirl filling, the bagels got through boiling and baking just fine.
No bagels were harmed during the testing of this recipe.

Yes, they’re super easy to veganize! Use a vegan block butter or margarine instead of butter, and replace the honey in the dough with maple syrup or additional brown sugar. Still delicious!

Flip them! If you find that the shaped bagels stick to the parchment paper, cover them with a second sheet of parchment paper, and place another baking sheet (or large tray etc.) on top. Flip the whole thing upside down carefully. Remove the sheet that’s now on top and carefully peel back the first baking paper. Proceed with boiling as usual.

If you make these cinnamon-swirled pumpkin sourdough bagels…

I’d love to hear how they turned out!

P.S. If you love making better-for-you versions of cozy classics, you might enjoy these recipes too:

happy baking!

Cinnamon-Swirled Pumpkin Sourdough Bagels with Fresh-Milled Flour

Soft, chewy, and naturally leavened, these cinnamon pumpkin sourdough bagels are made with fresh-milled whole grain flour, pumpkin puree, and a cozy swirl of buttery cinnamon sugar filling. A twist on the classic bagel, they combine the comforting flavors of a cinnamon roll with the wholesome goodness of whole grain sourdough. Perfect for cozy fall mornings, brunch, or as a make-ahead breakfast, these bagels are a healthier option that keeps you full and satisfied. Vegan-friendly and sourdough discard options available.
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Whole grain fresh-milled pumpkin sourdough bagels served in a basket lined with an embroidered linen cloth. One bagel is split to expose the dark brown cinnamon sugar swirl.
5 from 1 vote
Prep Time:15 minutes
Cook Time:20 minutes
Bulk Rest and Proofing Time:9 hours
Total Time:9 hours 35 minutes
Servings:8 bagels
Calories:305kcal
Equipment
  • stand mixer (optional) - You can also knead by hand, of course.
  • rolling pin - For rolling out the dough into an even rectangle.
  • large pot - For boiling the bagels before baking.
  • slotted spoon - For carefully lifting the cooked bagels out of the hot water.
Ingredients

Bagel Dough Ingredients

  • 500 g fresh-milled spelt flour - (Milled from 2¾ cups whole spelt berries.) Swap store-bought whole grain spelt flour.
  • 200 g water - (¾ cup + 1½ tbsp)
  • 125 g sourdough starter, active and bubbly - (½ cup)
  • 130 g pumpkin puree, homemade or from a can - (½ cup)
  • 45 g honey - (2 tbsp)
  • 10 g salt

Cinnamon-Swirl Ingredients

  • 55 g butter - melted and cooled, (4 tbsp)
  • 75 g brown sugar - (5½ tbsp)
  • 1 tbsp ground cinnamon
Instructions

Mix and rest the Dough

  • To the bowl of a stand mixer add water, pumpkin puree, sourdough starter, honey and salt.
  • Weigh out whole spelt berries and grind them on the finest setting of your grain mill. You can mill the flour right into the bowl with the wet ingredients. Use the paddle attachment to mix the dry and wet ingredients until there are no dry bits of flour on the bottom of the bowl. Cover and rest for 30 minutes to properly hydrate the flour.

Knead the Dough

  • Switch to the dough hook and knead the dough for 7 minutes on the lowest speed. It should come together into a smooth, firm but pliable ball. Cover and bulk ferment for 6-8 hours, until the dough is puffy and about doubled in size.

Roll Out and Shape Bagels

  • When the dough has doubled in size, stir together melted butter, sugar and cinnamon. It should be thick and spreadable.
  • Lightly flour your worktop and the top of the dough with flour. Roll the dough out into as neat a rectangle as you can. Spread the cinnamon filling evenly across the dough. Divide the dough into four equal parts, then cut each new rectangle into two triangles. Roll up each triangle from the tip towards the long side.
  • Take the rolled up piece of dough into your hands and gently press down from the middle out towards the end, to create a longer rope. Wrap the dough around your fingers and gently press the ends together until sealed. Place the shaped bagels onto a baking sheet lined with baking paper. Cover with plastic wrap and let them rise for 1-2 hours, or until the bagels are puffy but not doubled again.

Boil and Bake Bagels

  • Preheat the oven to 210°C (410°F). In a large pot, bring 2 litres (8 cups) of water to a boil. Add 1 tablespoon sugar and 1 tablespoon baking soda (and enjoy the cauldron bubble). Turn the heat down to a simmer. Gently lower two bagels at a time into the simmering water and boil for one minute. Flip once and boil the other side for another minute.
  • Carefully lift out the boiled bagels with a slotted spoon and place them back on the baking sheet. Once all bagels are boiled, bake for 20-25 minutes, or until the bagels turn golden brown. Place the sheet on a cooling rack and let the bagels cool down.
Notes
  1. Instead of active starter, you can use sourdough discard from the fridge and add 1 sachet (7g) of instant yeast. Let the dough rise for 1 hour before shaping, then rise for about 30 minutes before boiling.
  2. Don’t roll the dough too thin, or the layers might tear during shaping or boiling.
  3. Instead of pulling the dough to stretch it, hold it in both hands and gently press outward from the center to elongate into a rope. If the dough resists stretching, pause and just hold it as is for 10-15 seconds, until you feel it relax.
  4. Don’t roll the ends of the rope together, but gently press them together for 15–20 seconds to seal instead.
  5. The kneaded dough should be firm but pliable. There will be additional moisture from the butter in the filling and from boiling, so don’t add more water to the dough.
  6. The cinnamon sugar filling should be thick and spreadable, not wet and soupy. If the filling is too loose, place it in the fridge for 5-10 minutes.
  7. Store at room temperature, well wrapped, for up to 2 days. If you have any leftovers on day 2, split sourdough bagels and separate halves with a piece of parchment paper. Place in a freezer bag and press out as much air as possible. No need to thaw, just toast from frozen.
  8. For vegan cinnamon pumpkin bagels, swap vegan butter and maple syrup.
For more tips and swaps, check out the post above.
Author: Sarah | Grains & Greens Kitchen
Calories: 305kcal
Tried this recipe?Let me know how it turned out!

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Whole grain fresh-milled pumpkin sourdough bagels served in a basket lined with an embroidered linen cloth. One bagel is split to expose the dark brown cinnamon sugar swirl.

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5 from 1 vote

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3 Comments

  1. 5 stars
    These are very good! The dough was a dream to work with. However, I suspect that I rolled it out too thin in parts because it was difficult with some of them to get them off the paper on the baking sheet. I will make these again and work on the thickness when rolling them out. Or maybe it was because I put them in the oven with a hot water bottle to speed up the second rise because I was running out of time although that usually works great🤔

    Reply

      1. Homemade and it is really dry so to speak🤷 I will just try them again and they tasted good anyways😃

        Reply