Unique Fall Sourdough Recipes with Fresh Milled Flour
Cozy up your baking vibes this season with fall sourdough recipes made with fresh milled flour—from pumpkin cinnamon rolls to apple cider muffins. If the crisp fall air has you daydreaming about pumpkin spice and patches, you’re not alone. This roundup is a collection of some of my favorite sourdough recipes featuring whole grains, which I hope you’ll have on repeat this season.
There’s something extra special about using freshly milled whole wheat flour in your sourdough treats—it elevates flavor, brings wholesome nutrients, and makes every bake feel like a warm hug from the inside out with its unique flavor. Using sourdough discard and active starter is a great way to spend your time baking this fall. It’s not all pumpkin pie spice, either; we’ve got both sweet and savory ideas for you!
Grab your apron, maybe heat up a mug of cider or hot cocoa, and let’s dive into doughy, fall-flavored goodness for your next loaf of bread or batch of muffins.
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Why You’ll Love These Fermented Fall Bakes
Fresh-milled flour is like coffee beans straight to the grinder. Nutty, fragrant, and you’ll wonder why store-bought flour ever entered your life. These recipes feel like fall in every bite and are perfect for sharing with friends and family. From cozy pumpkin rolls to apple-spiced popables, each recipe has that autumn-ness you love about sweater weather.
Milling your own flour, kneading your own bread dough, and enjoying your loaves of sourdough bread will be your favorite hobbies this fall. Use your own sourdough starter to get the tangy, light bounce of sourdough and combine it with the unique depth of flavor and nutritional boost from milling your own wheat. That’s a win-win for taste, texture, and gut happiness!
From whole wheat sourdough bread loaves to cookies to rolls, you’ll find different bakes that will please everyone. New to milling your own grains? Check out our Fresh Milled Flour 101 guide to learn the basics on how to bake sourdough with freshly milled flour, including the health benefits.
Tools & Ingredients for Fall Sourdough Recipes
For these fall sourdough fresh-milled flour recipes, you’ll need a few basics. This is a quick list; there may be additional items and ingredients needed for each recipe, but this will get you most of the way! For best results, always mill your flour fresh for baking.
Tools
- Grain Mill
- Danish Dough Whisk
- Mixing bowls
- Spatulas
- Dough Scraper
- Food Processor
- Kitchen scale
- Silicone Baking Mats or Parchment Paper
- Loaf Pan, Baking Sheets, Muffin Tin, or Baking Pans
Pantry Star Ingredients
- Wheat Berries (check out our favorite grains for fresh milled whole grain flour, from hard red to soft white to rye flour)
- Active sourdough starter or discard
- Pumpkin puree (for those pumpkin-y bakes)
- Apples, apple pie filling, or apple cider (for the apple-spiced goodies)
- Classic homey spices: cinnamon, nutmeg, cloves, pumpkin spice
- Herbs and garlic for savory bakes
- Brown sugar, honey, or maple syrup
Sourdough Pumpkin & Herb Focaccia
This rustic fall sourdough loaf is a cozy fall twist on a classic bread, made with nutrient-rich fresh-milled flour. Pumpkin puree keeps the crumb tender and moist, while fresh or dried herbs like rosemary, sage, and thyme add an irresistible savory aroma. Baked to golden perfection, this focaccia recipe is perfect for pairing with all of those warm soups ahead, as an appetizer, or just enjoyed warm from the oven. Get the recipe here.
Sourdough Challah Bread
This sourdough challah bread transforms the traditional enriched loaf into something truly special and super flavorful, thanks to the fresh-ground whole wheat. The dough is enriched with butter, eggs, honey, and oil. The starter lends a tang and heartiness to this soft and slightly sweet bread. Braided and finished with a glossy egg wash, you’ll love serving it for special occasions, brunch, or just when you want a beautiful bake. Get the recipe here.
Apple Pie Oat Bars with Discard
This recipe is perfect for autumn sourdough baking. They are easy to whip up, have those warm spices you love about fall, and have wholesome whole grains and oats. Using sourdough discard adds moisture and a subtle tang, and the fresh milled flour brings nuttiness and extra nutrition. Perfect for on-the-go snacks, a fun dessert, or even breakfast. Get the recipe here.
Sourdough Pumpkin Pie Focaccia
This recipe brings everything cozy about pumpkin pie into a shareable loaf. Using fresh ground flour for depth and nutty undertones, this dough is enriched with pumpkin puree, maple syrup, and warm fall spices. A brown sugar and butter crumble, along with a light glaze on top, gives it a sweetness without going overboard. Perfect for brunch, dessert, or a fall afternoon treat. Get the recipe here.
Sourdough Apple Pie Cobbler
This rustic dessert turns apple pie filling (canned or homemade) into a warm, comforting treat perfect to end any fall meal. Discard gives the cobbler a subtle tang to the biscuit-like topping. Sweetened with maple syrup and brown sugar, this gorgeous bake is golden and bubbly. Easy to assemble, no rolling pin or pie crust needed, this is perfect anytime you’re craving a homey and satisfying treat. Get the recipe here.
Sourdough Apple Cider Mini Muffins
Bite-sized flavor that feels like a crisp autumn morning in every morsel. A perfect balance of sweet and tangy, these tender, golden, mini muffins are super quick to throw together and ideal for on-the-go breakfasts or snacks. Get the recipe here.
Sourdough Pumpkin Cinnamon Rolls
These delicious rolls combine pumpkin-infused dough with fresh milled whole wheat and sourdough for some slightly spiced, warm, and pillowy buns. They are indulgent and sweet, perfect for any fall morning. Baked until perfectly golden, then topped with an irresistible cream cheese frosting, they’ll make your weekend that much better! Get the recipe here.
Sourdough Pretzel Bites
These sourdough pretzel bites pack warm, chewy satisfaction into miniature form. They have a hearty flavor and nutritional perks from whole wheat. They’re great for dipping and sharing, and are perfect when you’re hosting a tailgate or gathering for appetizers. Easy to munch and hard to resist! Get the recipe here.
Sourdough Discard Ricotta Donuts
These little Italian-style donuts (zeppole) deliver a crispy outside and a tender inside. They’re rich, moist, and melt in your mouth. No yeast or rise times needed, these dough-balls are super easy to whip up. Perfect for a fun and special, but quick, little weekend breakfast or impromptu dessert. Fried until just golden, you can dust with powdered sugar, cinnamon-sugar, or add a little glaze. Get the recipe here.
Sourdough Chocolate Chip Banana Muffins
These yummy muffins marry those overripe bananas on your counter with chocolate chips and a little sourdough discard. You’ll get fluffy, indulgent, and wholesome muffins that are great for breakfast, snacks, and on-the-go. The blend of different wheats gives these guys a slightly nutty, but smooth flavor. It’s your favorite flavors, elevated. Get the recipe here.
Sourdough Cheesy Focaccia
This bread brings together the best of classic comfort: Cheese and Garlic. Cheese-topped focaccia made with nutty whole wheat, crispy edges, and a tender crumb will have you baking this over and over. Whether you pull it apart for dipping, use it for sandwiches, or serve it with salads, it’s sure to hit the spot every time. Get the recipe here.
Sourdough Discard Pound Cake
This delicious pound cake blends the buttery richness of the classic dessert with a subtle sourdough tang and the deep, nutty tones of fresh milled wheat. With sourdough discard and Greek yogurt, you’ll get a super moist and lush batter that bakes up to golden perfection with that tell-tale split down the middle. Ideal for family gatherings, potlucks, fondue, teatime, or just when you want to bake a simple yet elegant treat. Try it with whipped cream & berries or toasted with jam for breakfast. Get the recipe here.
Sourdough Chocolate Chip Cookies
These are the most irresistible soft chocolate chip cookies made with fresh milled flour and sourdough discard. They are rich, nutty, and have just a slight hint of tang. The dough gets chilled for 24 hours for ultimate flavor and fermentation. These cookies come out tender and chewy every time and are perfect for sharing (or keeping to yourself). You may never go back to regular chocolate chip cookies! Get the recipe here.
Sourdough Pretzel Buns
These pretzel buns blend whole wheat with sourdough for a deep, nutty flavor to deliver a roll that’s tender on the inside and has that classic pretzel skin on the outside. Baked to perfection, these buns are perfect for burgers, sandwiches, or just on their own. Impress your tailgating buds, football fans, or grilling family. Get the recipe here.
Pumpkin Mac & Cheese with Sourdough Roux
A twist on the classic favorite, this recipe sneaks in veggies and uses up some sourdough discard! You’ll have a rich pasta sauce perfect for any fall dinner as the main guest or a side. Creamy, hearty, and with just the right amount of pumpkin flavor, it’s great for parties, game days, or whenever you need a comforting (and easy) meal that still feels special. Get the recipe here.
Sourdough Discard Pumpkin Bread
This delicious and easy sourdough discard pumpkin bread recipe will be on repeat this season for your family. Moist, warm, and cozy pumpkin spice will have you singing its praises at breakfast and snack time! Get the recipe here.
Sourdough Apple Pie Cupcakes
A twist on the classic apple pie, these cupcakes will have you delighted. This recipe blends cozy fall flavors with sourdough discard and fresh milled flour to create tender, moist apple pie cupcakes. It’s a clever way to use up discard while elevating a classic dessert with whole grain depth and tang. Get the recipe here.
Sourdough Discard Pumpkin Cinnamon Sticks
A cozy fall recipe for sourdough discard pumpkin cinnamon sticks made with freshly milled flour. These treats combine pumpkin purée, sourdough discard, Greek yogurt, and warm spices into a quick, enriched dough that’s rolled, topped with pumpkin spice sugar, baked until golden, and finished with a maple cream cheese glaze. Get the recipe here.
So there you have it—some fun whole grain bread recipes starring your fresh ground flour and sourdough starter ferments. Whether it’s pumpkin cinnamon rolls that vanish in minutes or mini muffins that spark “oohs” from your family, you’re serving up comfort with a whole lot of charm.
Now go put on your favorite sweater, crank up the oven, and get ready for some fall baking. What’s your favorite whole wheat sourdough recipe?
Want more fall recipe inspiration? Try making Maple Pumpkin Custard, Pumpkin Cake Cookies, Roasted Pumpkin Seeds, Zucchini Muffins, Banana Blondies, or Roasted Beet Pasta Sauce.
FAQs for Fall Sourdough Recipes with Fresh Milled Flour
It’s like swapping instant coffee for freshly ground beans—you taste the real flavor, you get more nutrients, and every loaf smells like wow. Fresh flour retains the germ and bran, so your sourdough isn’t just tasty—it’s less processed and more beautiful inside and out.
Totally. In the more relaxed recipes (like bars or cookies), discard adds tang and helps you reduce waste—and the fall spices usually steal the show anyway. For breads you’ll want an active starter to help rise faster.
Just your standard baking gear and whatever you use to mill your flour. A mixer and kitchen scale always help, but are not required.
This collection is such a wonderful celebration of seasonal baking. From sweet treats to savory breads, each recipe feels like it was made to bring people together. Thanks for this!
These are all amazing, I don’t know which one to make first!!
All of these recipes sound delicious. Sourdough bread is my absolute fave!!