Gluten-Free Bakeries Across Wisconsin: Your Complete Guide

Wisconsin families managing celiac disease or gluten sensitivity finally have real options. Across the Badger State, more than 30 dedicated gluten-free bakeries and dozens of conventional bakeries with excellent GF offerings now serve everything from fresh bread and donuts to elaborate wedding cakes. This guide covers every region—from Milwaukee's thriving GF scene to hidden gems in the Northwoods—with the practical details you need to plan visits with confidence.

The landscape has transformed dramatically since 2020, with dedicated facilities opening in unexpected places like Rhinelander and Bloomer. Whether you're a local seeking your weekly bread or a family planning a Door County vacation, these bakeries prove that gluten-free no longer means going without.

More sweet treat guides:

Milwaukee’s best cupcakes

The best pies in Greater Milwaukee

Milwaukee metro: The state's deepest options

The Milwaukee area offers Wisconsin's most concentrated collection of dedicated gluten-free bakeries, making it the state's safest region for families with celiac disease.

Blooming Lotus Bakery — Milwaukee

100% Dedicated Gluten-Free | Also free of grain, dairy, eggs, cane sugar, oils, soy, and yeast

This dual-location bakery represents the gold standard for allergen-conscious families. Everything is made with nut and seed flours, creating naturally high-protein, low-carb treats that work for diabetic, paleo, and celiac diets simultaneously. The daily fresh-baked bread, muffins, scones, and biscotti draw loyal customers from across southeastern Wisconsin.

• East Side: 2215 East North Avenue, Milwaukee | (414) 212-8010

• Shorewood: 3948 North Maryland Avenue | (414) 800-5030

• Website: blbmke.com

MOR Bakery & Cafe — Milwaukee

100% Dedicated Gluten-Free | Vegan options available

Founded by a mother whose son had severe food issues, MOR operates from a dedicated gluten-free commercial kitchen in a refurbished industrial warehouse. Their weekly pre-order menu features small-batch baked goods using organic, locally-sourced ingredients. The cafe atmosphere and farmer's market presence make this feel like a community gathering spot rather than just a bakery.

• Location: 5504 W. State Street, Milwaukee

• Walk-in Hours: Fridays 11am-5:30pm, Saturdays 9am-1pm

• Farmers Market: South Shore Farmer's Market (seasonal Saturdays 8am-12pm)

• Ordering: Sign up for email list at morfoodsmke.com for weekly menu access

• Website: morfoodsmke.com

Molly's Gluten-Free Bakery — Pewaukee

100% Dedicated Gluten-Free AND Nut-Free

For families managing multiple allergies, Molly's stands out as one of Wisconsin's only dedicated bakeries that's both gluten-free and nut-free. With over 10 years in business, they've earned Neighborhood Favorite awards in 2018, 2019, and 2023. Their product range spans breads, bagels, English muffins, cakes, pies, and cookies—with customization available for additional allergens including coconut, soy, and dairy.

• Location: N47 W28270 Lynndale Rd (Hwy JK), Pewaukee

• Ordering: Order ahead required—check website for pickup times

• Shipping: Some items ship within Wisconsin

• Website: mollysglutenfreebakery.com

MyBread Bakery — Racine (Retail Products)

100% Dedicated Gluten-Free, Vegan, Non-GMO, Top-8 Allergen Free

Founded by Dan Gallagher, who has celiac disease, MyBread operates as a wholesale bakery producing bread loaves, slider buns, and soft pretzels distributed to grocery stores across Wisconsin and beyond. While there's no retail storefront, you can find their products at Woodman's, Walmart, Fresh Thyme (Kenosha), and O&H Danish Bakery locations.

• Production Facility: 1841 Douglas Ave, Racine

• Website: mybreadbakery.com

Additional Milwaukee Area Options

O&H Danish Bakery (Racine) produces gluten-free Kringle—Wisconsin's iconic pastry—in a separate dedicated GF facility. Their GF pecan and apple Kringles ship nationwide. Multiple locations including 5910 Washington Avenue, Racine. Website: ohdanishbakery.com

Cranky Al's (Wauwatosa) offers gluten-friendly donuts daily at 6901 W North Ave. Important note: NOT celiac-safe due to shared fryer equipment—suitable only for gluten sensitivity. Hours: Tuesday-Sunday 6am-1pm.

The Bread Pedalers (West Allis) at 1436 S 92nd St features GF biscuits, Friday cinnamon rolls, and rotating GF treats. Run by professional cyclist sisters. Not celiac-safe but good protocols. Phone: (414) 509-5198.

Madison's GF scene rivals any Midwest city

Madison punches well above its weight with multiple dedicated facilities and earned a ranking as #100 globally for gluten-free dining with seven dedicated GF establishments.

Madison Chocolate Company — Madison

100% Dedicated Gluten-Free | Award-Winning Chocolatier

The croissants here have been described as "better than pastries in 12 European countries"—and they're completely gluten-free. This woman-owned chocolate shop and café produces everything in-house in a dedicated GF facility, from legendary ham & Gruyère croissants to Good Food Award-winning passion fruit caramels. Weekend waffles at the Glenway location are worth planning around.

• Glenway (Original): 729 Glenway St, Madison | Weekend waffles

• Odana (Larger): 5521 Odana Rd, Madison | More selection

• Hours: Mon-Fri 7am-6pm, Sat-Sun 8am-5pm

• Phone: (608) 286-1154

• Website: madisonchocolatecompany.com

Paleo Mama Bakery — Madison

100% Dedicated Gluten-Free | Paleo, Keto, Vegan Options

Starting with 20 products in 2014, Paleo Mama now offers over 70 gluten-free items and supplies more than 20 stores and restaurants throughout Wisconsin and Illinois. Their retail storefront carries over 300 items including breads, cupcakes (the vanilla salted caramel is legendary), cookies, whoopie pies, pizza, frozen meals, and even ice cream. They're regular vendors at the Dane County Farmers' Market on Saturdays.

• Location: 961 S. Park Street, Madison

• Phone: (608) 230-5253

• Website: paleomamabakery.com

goodAFbaking — Madison

100% Dedicated | Free of ALL Top-9 Allergens

For families managing multiple food allergies, goodAFbaking offers something rare: a bakery that's completely free of wheat/gluten, dairy, eggs, tree nuts, peanuts, soy, sesame, and artificial dyes. Their artisan bread loaves, bagels (plain, onion, everything), cookies, and layer cakes are available through online ordering with pickup or at pop-up markets.

• Ordering: goodafbaking.com

• Products: Bread loaves ($11), bagel 6-packs ($24+), layer cakes (from $50)

• Email: goodafbaking@gmail.com

Sweeternative Baking & Haven Gluten Free — Madison

Two additional dedicated GF bakeries focus on custom celebration and wedding cakes. Sweeternative Baking (sweeternativebaking.com) operates from a dedicated GF kitchen and supplies local coffee shops. Haven Gluten Free specializes in custom orders for weddings and events. Both require advance ordering.

Bloom Bake Shop — Madison

Not Dedicated but Excellent GF Options

Bloom maintains a separate display case for their extensive GF/vegan selection including cupcakes, cake donuts, brownies, whoopie pies, and scones. While not a dedicated facility, many celiac customers report eating safely here due to their careful protocols. Their GF wedding cakes receive particular praise.

• Location: 1851 Monroe St, Madison

• Website: bloombakeshop.com

The Fox Valley surprises with dedicated bakery excellence

The Appleton-Oshkosh corridor has quietly become one of Wisconsin's best regions for celiac-safe baking, with four dedicated gluten-free bakeries within a 30-mile radius.

Happy Bellies Bake Shop — Appleton

100% Dedicated Gluten-Free | Also Dye-Free, Non-GMO, All-Natural

This dedicated bakery has earned cult status for its fresh donuts—Blue Moon, Vanilla Sprinkle, Chocolate, and seasonal flavors like Gingerbread and Peppermint Mocha. Beyond donuts, they offer custom cakes, cupcakes, scones, muffins, cinnamon rolls, and Friday-only hot pretzels. The full espresso bar with homemade syrups makes this a destination. They ship donuts to 14 states for families who can't visit in person.

• Location: 2107 N. Richmond Street, Appleton

• Phone: (920) 730-2253

• Hours: Tue-Wed 7am-2pm, Thu 7am-6pm, Fri-Sat 7am-2pm, Sun-Mon closed

• Pre-order: Available online

• Website: happybelliesbakeshop.com

Cornflower Cafe (Ann's Gluten Free Bakery) — Appleton

100% Dedicated Gluten-Free | Full Cafe Experience

This cozy café combines a dedicated GF bakery with full breakfast and lunch service. Their cheddar herb bread draws particular praise, along with fresh scones, muffins, brownies, and cinnamon rolls. The refrigerator/freezer case offers ready-made take-and-bake pizzas and soups for busy families.

• Location: 3414 W. College Ave, Appleton

• Phone: (920) 939-2027

• Hours: Mon 9am-3pm, Tue-Fri 9am-6pm, Sat 9am-3pm, Sun closed

Sweet Jules Bakes — Oshkosh

100% Dedicated Gluten-Free | Accommodates Big-9 Allergies

The first bakery in Winnebago County where everything in the shop is gluten-free. Owner Jules employs staff members with celiac disease who test products. The '50s-themed decor and beautifully decorated cupcakes make this worth the trip. Find their products at the Oshkosh Food Co-Op and seasonal farmers markets in Oshkosh and Neenah.

• Location: 9 Church Avenue, Oshkosh

• Hours: Thursday-Saturday (confirm current hours)

• Website: sweetjulesbakes.com

Naturally Delightful — Green Bay

100% Gluten-Free, Vegan, and Organic | Wide Distribution

This Green Bay-based bakery specializes in elaborate custom decorated cakes, cupcakes, cookies, and donuts—all 100% gluten-free, soy-free, and dairy-free. While custom orders are their specialty, you can find their products at Festival Foods locations throughout Northeast Wisconsin (Green Bay, De Pere, Suamico, Appleton, Fond du Lac, Oshkosh, Sheboygan, New London), Woodman's Markets, and several Door County locations.

• Phone: (920) 265-9879

• Website: naturallydelightfulcreations.com

Fox Valley bakeries with GF options

Tamara's The Cake Guru (Oshkosh) offers over 500 cupcake flavors with GF options now individually packaged. Their "Four-less" flourless cupcakes are a specialty. Call ahead: (920) 236-9144. Website: cakeguru.com

Uncle Mike's Bake Shoppe (multiple Green Bay locations) and Manderfield's Home Bakery (Appleton, Menasha) stock GF items in freezer cases.

Door County requires seasonal planning

Door County's tourist-driven economy means many bakeries close or reduce hours from November through April. Plan accordingly and always call ahead during shoulder seasons.

Sweetie Pies — Fish Creek

This beloved pie shop produces four gluten-free pie varieties: Cherry, Apple, Blueberry, and Strawberry-Rhubarb. GF pies are made on a dedicated day with dedicated utensils before regular production begins. Available whole or by the slice during their limited seasonal hours.

• Location: 9106 State Hwy 42, Fish Creek (at Settlement Shops)

• Phone: (920) 868-2743

• Seasonal Hours: Daily 10am-4pm Memorial Day through October; weekends only November through mid-February; CLOSED mid-February through mid-April

• Website: sweetiepiesdoorcounty.com

Blue Horse Beach Cafe — Fish Creek

Open 361 days per year, this year-round café offers GF bagels, buns, and pastries from Naturally Delightful bakery. Important caveat: staff acknowledge cross-contamination risk for items prepared in-house. Stick to pre-packaged items from the dedicated bakery for celiac safety.

• Location: 4113 Main St, Fish Creek

• Phone: (920) 868-1471

• Hours: Daily 7am-5pm year-round

• Website: bluehorsecafe.com

Zero Sum Door County (Fish Creek/Sister Bay area) operates as a dedicated gluten-free eatery where celiacs can feel completely safe. Kick Ash Coffee in Sister Bay reportedly has an all-GF bakery section.

Western Wisconsin offers surprising gems

From the Coulee Region to the St. Croix Valley, Western Wisconsin has developed a strong network of dedicated GF bakeries—many started by families managing celiac disease themselves.

Omega Bakery — Holmen (La Crosse Area)

100% Dedicated Gluten-Free & Allergen-Friendly

With over 250 items including scones, cakes, cupcakes, donuts, cookies, and breads, Omega offers the widest selection in western Wisconsin. They also accommodate dairy-free, nut-free, soy-free, and vegan diets—making this ideal for families managing multiple restrictions.

• Location: Holmen, WI (serving the Coulee Region/La Crosse area)

• Website: omegabakerywi.com

Jonnie's Bakery — Eau Claire

100% Dedicated Gluten-Free Since 2020

Operating from a commercial kitchen that's been completely gluten-free since 2020, Jonnie's offers cookies (chocolate chip, lemon lavender, monster), mixed berry scones, cake donuts, and dark chocolate quinoa bites. Many items are also dairy-free and vegan. Find them at the Downtown Eau Claire Farmers Market on Saturdays or arrange kitchen pickup.

• Location: 930 Galloway St, Eau Claire (Banbury Place, Building 13, Suite 214)

• Email: thepretentiousbaker@gmail.com

• Website: jonniesbakery.com

Get Baked, LLC — Bloomer (Chippewa Valley)

100% Dedicated Celiac-Safe Home Bakery

This new (2024) cottage bakery was started by an owner whose family member has celiac disease—no gluten ever enters the kitchen. Look for their holiday specialties including gingerbread house kits and Christmas cookie boxes at pop-ups at the Wisconsin Farmers Union headquarters, Market on River in Chippewa Falls, and Down to Earth Garden Center in Eau Claire.

Wild Flour Bakery — Chippewa Falls

100% Dedicated Gluten-Free Home Bakery

Owner Alyssa Gilliam started baking after her son was diagnosed with a gastrointestinal disorder requiring gluten-free eating. Her home-based bakery produces unprocessed, gluten-free baked goods.

St. Croix Valley options

For families in the Hudson/River Falls area, Sift Gluten Free in Minneapolis (25-30 minutes from Hudson) offers the region's best dedicated GF bakery experience with donuts, scones, cinnamon rolls, and custom cakes. Their products are also carried at Hudson Grocery and other local retailers. Website: siftglutenfree.com

Sweet Beet Bakery (137 S Knowles Ave, New Richmond) offers 3-4 rotating GF items daily including cinnamon rolls and cupcakes. Not dedicated but supplies GF items to local cafes. Hours: Thu-Sun 7am-1pm. Phone: (715) 246-9866.

Linda's Bakery (190 E City Highway 16, West Salem) has served the La Crosse area since 1973 with "gluten-friendly" cakes and pastries. Delivers within 50 miles. Not celiac-safe due to shared facility. Phone: (608) 786-1818.

Wisconsin Dells

Sandy Kakes (329 Broadway, Wisconsin Dells) offers gluten-free and vegan custom cakes, cupcakes, and desserts for special occasions. Everything made fresh to order with delivery available across several counties. Hours: Thu 7am-4pm, Fri-Sat 7am-7pm, Sun 7am-5pm. Phone: (608) 697-8198. Website: sandykakes.com

The Northwoods now has dedicated options

For years, Northern Wisconsin was a desert for celiac families. That's changed with the opening of Almond & Berry in Rhinelander—now one of the state's best dedicated bakeries.

Almond & Berry — Rhinelander

100% Dedicated Gluten-Free | Celiac-Safe

This mother-daughter owned bakery opened in 2024 specifically because the owner's 8-year-old daughter Kate has celiac disease. The cinnamon rolls have achieved legendary status—customers drive hours for them. The full café offers baked goods, smoothies, and a juice bar, all completely safe for celiac diners. As one parent wrote: "It's such a rare treat to be able to tell my celiac son that he can pick anything he wants from the case!"

• Location: 310A N. Brown Street, Rhinelander

• Phone: (715) 401-2535

• Hours: Mon-Fri 7am-4pm, Sat-Sun 8am-2pm (year-round)

• Website: almondandberry.square.site

Nui Thai House/Coffee House — Woodruff

100% Dedicated Gluten-Free Kitchen

The owner's husband has celiac disease, so the entire kitchen operates gluten-free. Beyond Thai dishes like Pad Thai and spring rolls, they offer flatbreads, baked goods, and Thai tea drinks. Critical note: very limited hours (Wed-Thu 11am-5pm)—always call ahead.

• Location: 1203 1st Ave, Woodruff

• Phone: (715) 358-0563

Schroeter's Gluten Free Bakeshop — Woodruff

100% Dedicated Facility | Wholesale Focus

This family-owned bakery (with celiac in the family) produces what many consider the best GF pizza crusts in Wisconsin. While primarily wholesale—products available at retailers like Outpost—they also make cookies and whoopie pies. Not a walk-in bakery.

• Website: schroetersglutenfreebakeshop.com

Additional Northern Wisconsin options

Boulder Junction Coffee Company (10362 Main St, Boulder Junction) offers GF muffins and English muffins for breakfast sandwiches in a beautiful Northwoods setting. Not dedicated but uses separate pans and timing. Open daily 6am-3pm. Phone: (715) 385-2655.

Nanette's Kitchen (Minocqua) offers both GF and regular baked goods—but operates seasonally only (July-September). Need 14 days advance notice for special orders. Website: nanetteskitchen.net

For families visiting the Superior area, Gluten Free Duluth (3002 West 3rd Street, Duluth, MN) operates a dedicated cottage bakery with sourdoughs, muffins, donuts, and treats. Give one week notice for orders. Website: glutenfreeduluth.com

Central Wisconsin has room to grow

Wausau and Stevens Point offer fewer dedicated options, but several cafes accommodate gluten-free diets well.

Zest Bakery and Coffeehouse (624 Isadore St, Stevens Point) offers GF bread upgrades for sandwiches and keeps GF items in the display case. Staff are knowledgeable—when you mention celiac, they'll prepare sandwiches on a separate clean grill. Phone: (715) 344-6185.

Downtown Grocery Bakeshop (607 N Third St, Wausau) stocks select items made without gluten or dairy. Hours: Mon-Sat 9am-8pm, Sun 11am-5pm. Phone: (715) 848-9800.

Patina Coffeehouse (Wausau area) serves homemade GF cookies, scones, and breakfast wraps.

Practical planning tips for Wisconsin GF families

For celiac disease (need dedicated facilities): The safest bakeries statewide are Blooming Lotus, MOR Bakery, Molly's (Milwaukee area); Madison Chocolate Company, Paleo Mama, goodAFbaking (Madison); Happy Bellies, Cornflower Cafe, Sweet Jules, Naturally Delightful (Fox Valley); Omega Bakery, Jonnie's Bakery (Western WI); and Almond & Berry (Rhinelander).

Order-ahead requirements vary significantly. Molly's Gluten-Free Bakery requires advance orders. MOR Bakery's pre-order menu opens Sunday-Tuesday each week. Custom cakes typically need 1-2 weeks notice. Farmers market vendors require timing your visit to market days.

Seasonal considerations matter. Door County bakeries often close mid-February through mid-April. Northwoods businesses reduce winter hours. Always call ahead October through May.

Farmers markets expand your options. Paleo Mama (Dane County Farmers' Market), Sweet Jules (Oshkosh/Neenah markets), Jonnie's Bakery (Downtown Eau Claire market), and MOR Bakery (South Shore Farmer's Market) all vend seasonally.

"Gluten-friendly" means cross-contamination risk. Bakeries using this term (Cranky Al's, Linda's Bakery, Blue Horse Beach Cafe, and others) are suitable for gluten sensitivity but not celiac disease. When in doubt, ask specifically about dedicated equipment and preparation protocols.

Conclusion

Wisconsin's gluten-free bakery landscape has never been stronger. From dedicated facilities producing artisan croissants in Madison to a mother-daughter team serving legendary cinnamon rolls in Rhinelander, families managing celiac disease can now find safe, delicious baked goods in nearly every corner of the state. The key is knowing which bakeries operate dedicated facilities versus those offering "gluten-friendly" options—a distinction that matters enormously for celiac safety.

What stands out most is how many of these bakeries were started by families living with celiac disease themselves. That personal connection translates into genuine care about safety protocols and an understanding of what it means to finally bite into a donut or croissant without worry. Whether you're planning a Door County vacation, road-tripping through the Northwoods, or simply seeking your weekly bread closer to home, this guide should help you find bakeries worthy of your trust—and your taste buds.