Book The Best Hotels in Southeast Minnesota, MN for 2026 from CA $94 - Fully Refundable Options

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Go beyond your typical stay in Southeast Minnesota

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Our top choices for Southeast Minnesota hotels

A modern indoor patio with a fire feature, seating, and large windows.

A modern hotel lobby with a large glass wall, a green wall mural, and a seating area with sofas and chairs.

A modern living room with a fireplace, large windows, and a flat-screen TV mounted on the wall.

A reception area with a curved reception desk, wooden shelving, and a green moss wall with the text "I ♥ EVEN".

1. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

James

CA $160

CA $187 total

includes taxes & fees

Oct 23 - Oct 24

A modern dining area with high tables, chairs, and pendant lighting.

A hotel room with two beds, a desk with a computer, a chair, and a window with a view.

A swimming pool with a tiled deck, sun loungers, and a lifeguard chair.

A multi-story hotel with a modern design, featuring a prominent entrance with a covered area and a parking lot in front.

2. Hampton Inn & Suites Rochester-North

Rochester

Mark

CA $144

CA $166 total

includes taxes & fees

Nov 6 - Nov 7

A spacious outdoor dining area with modern furniture and large windows offering views of the city.

A modern interior with a wooden ceiling, a large black shelving unit, and a refrigerator stocked with beverages.

A reception desk with a modern design, featuring a wooden panel and a wall adorned with framed botanical artwork.

An outdoor dining area with wooden beams, tables, and chairs.

3. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

Naomi

CA $150

CA $173 total

includes taxes & fees

Nov 7 - Nov 8

A self-service breakfast station with a waffle maker, coffee machines, and a variety of condiments.

A reception area with a wooden reception desk, a red doormat, and framed awards on the wall.

A compact laundry area with a washing machine, dryer, and a water fountain.

A hotel room with a large bed, a desk, a chair, a television, and a window with curtains.

4. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $93

CA $107 total

includes taxes & fees

Nov 15 - Nov 16

A hotel room with a large bed, a desk with a chair, a window with a view of the outdoors, and two bedside lamps.

A snack bar with a variety of packaged snacks, a refrigerator stocked with beverages, and a microwave.

A hotel room with a desk, a chair, a flat-screen TV mounted on the wall, and a lamp on the desk.

A gym with treadmills, elliptical machines, and a stationary bike.

5. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Terri

CA $113

CA $131 total

includes taxes & fees

Nov 19 - Nov 20

A Holiday Inn Express building with a covered entrance, outdoor seating area, and a well-lit facade.

A hotel room with two beds, a desk, a chair, a television, and a kitchenette.

A hotel dining area with multiple tables and chairs, a coffee station, and a seating area with sofas.

A coffee station with two espresso machines and a variety of coffee pods and cups.

6. Holiday Inn Express & Suites Rochester – Mayo Clinic Area by IHG

Kutzky Park

Janet

CA $142

CA $164 total

includes taxes & fees

Nov 7 - Nov 8

A restaurant with wooden tables and bar stools, a bar area with a counter, and multiple televisions mounted on the walls.

A modern kitchen with wooden cabinets, a microwave, an oven, and a dishwasher.

A hotel room with two beds, a desk, a chair, and a mirror.

An indoor swimming pool with a slide, seating area, and a large frog statue.

7. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

blake

CA $103

CA $118 total

includes taxes & fees

Oct 25 - Oct 26

A hotel reception desk with a wooden counter, a computer, and a vase with flowers.

An indoor swimming pool with wooden beams and white chairs around it.

A hotel room with a large bed, a view through a sliding glass door to an outdoor area, a nightstand with a lamp, and a wooden headboard.

A living room with stone walls, a fireplace, leather furniture, and a ceiling fan.

8. Baymont by Wyndham Kasson Rochester Area

Kasson

Dana

CA $92

CA $99 total

includes taxes & fees

Oct 28 - Oct 29

A spacious lobby with a reception desk, sofas, and a coffee table.

A hotel room with a large bed, a sofa, a TV, and a desk.

An indoor swimming pool with clear blue water, surrounded by tiled flooring and equipped with a pool ladder.

A lobby with a brown sofa, yellow armchairs, a coffee table, and a clock on the wall.

9. Sleep Inn & Suites West-Near Medical Center

Rochester

Jacqueline

CA $111

CA $127 total

includes taxes & fees

Nov 15 - Nov 16

A modern hotel lobby with a reception desk, seating area, and a kitchenette.

A hotel with a covered entrance, multiple floors, and a parking lot.

A small, well-organized pantry with shelves stocked with snacks and beverages.

A modern hotel lobby with a reception desk, seating area, and a large window providing natural light.

10. Spark by Hilton Rochester South

Rochester

Stanton

CA $115

CA $132 total

includes taxes & fees

Nov 1 - Nov 2

A hotel entrance with a stone facade, a glass door, and a metal roof structure.

A spa area with a hot tub, exercise equipment, and a seating area with chairs and a table.

A hotel lobby with striped armchairs, a sofa, a fireplace, and a clock on the wall.

A hotel room with a kitchenette, a dining area with striped chairs, a sofa, a TV, and a window with curtains.

11. Aspen Suites

Rochester

Douangta

CA $189

CA $228 total

includes taxes & fees

Oct 29 - Oct 30

An outdoor seating area with a fire feature, blue cushioned chairs, and a modern building with large windows in the background.

A modern Hyatt House hotel with a prominent 'Hyatt House' sign, multiple floors, and a parking garage.

A modern bar area with seating and a counter.

A modern indoor pool area with lounge chairs and a pool.

12. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Elsie

CA $179

CA $206 total

includes taxes & fees

Oct 29 - Oct 30

An indoor swimming pool with a dolphin sculpture, wooden ceiling, and clear windows.

A hotel reception area with a red 'Hello' sign, a reception desk, a coffee station, and a fireplace.

A hotel reception area with a coffee station, seating area, and a fireplace.

A hotel room with a large bed, two bedside tables with lamps, a telephone, and a window with sheer curtains.

13. TownePlace Suites by Marriott Rochester

Rochester

Kari

CA $138

CA $159 total

includes taxes & fees

Oct 30 - Oct 31

A hotel breakfast area with a self-serve station, including a waffle maker, toaster, and various food items.

A modern living room with a sofa, coffee table, and a TV mounted on a stone wall.

A hotel lobby with a patterned carpet, two beige armchairs, a small table, a clock, a fire extinguisher, and a staircase.

A compact kitchen with a microwave, refrigerator, and coffee maker. A small bar stool is near the counter.

14. Quality Inn & Suites Mayo Clinic Area

Rochester

Jessica

CA $96

CA $112 total

includes taxes & fees

Nov 13 - Nov 14

An outdoor patio area with yellow umbrellas, wicker furniture, and a sign for Centerstone Plaza Hotel.

A garden with a water feature, rocks, and yellow umbrellas.

A modern living room with a dark wall, a decorative light fixture, and a patterned wall art piece.

A restaurant interior with wooden tables, chairs, and a stone wall.

15. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Deanna

CA $161

CA $185 total

includes taxes & fees

Oct 24 - Oct 25

An outdoor patio area with a concrete floor, wooden fence, and string lights.

A breakfast bar with a wooden counter, a coffee machine, and a refrigerator.

A modern living room with a stone fireplace, a blue armchair, a round coffee table, and a large window offering a view of the outdoors.

16. Fairfield Inn & Suites Rochester Mayo Clinic Area/St. Marys

Kutzky Park

Brien

CA $170

CA $195 total

includes taxes & fees

Nov 6 - Nov 7

An outdoor seating area with wooden pillars, colorful striped cushions, and potted plants.

A modern hotel room with a bed, desk, and kitchenette.

A modern lounge area with a sofa, chairs, and tables.

A modern restaurant with a counter, seating area, and a TV screen.

17. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

howard

CA $166

CA $191 total

includes taxes & fees

Nov 12 - Nov 13

A Comfort Inn hotel with a stone facade, a covered entrance, and a parking area.

A hotel room with a blue sofa, a wooden coffee table, a bed with white linens, a TV, and a large mirror.

A modern dining area with wooden tables and chairs, a kitchen with granite countertops, and a view of the outdoors through large windows.

A spacious living room with a stone fireplace, blue sofas, and a flat-screen TV.

18. Comfort Inn & Suites West - Medical Center

Rochester

Lori

CA $122

CA $141 total

includes taxes & fees

Nov 15 - Nov 16

An outdoor patio with a brick floor, stone fireplace, and wooden pergola.

A conference room with multiple tables and chairs, ceiling fans, and artwork on the walls.

A modern hotel lobby with a stone wall fireplace, comfortable seating, and a chandelier.

An indoor swimming pool with clear pool rules posted on the wall, a lifeguard chair, and a pool lift sign.

19. Homewood Suites by Hilton Rochester Mayo Clinic Area / Saint Marys

Kutzky Park

Lin

CA $166

CA $191 total

includes taxes & fees

Nov 6 - Nov 7

An indoor swimming pool with a curved design, surrounded by palm trees and a white pool ladder.

A modern hotel with a prominent neon sign, multiple floors, and a well-maintained lawn area.

A modern hotel lobby with a reception desk, a digital information kiosk, and a patterned floor.

A modern interior with a fireplace, a green armchair, and a patterned rug.

20. Treasure Island Resort & Casino

Welch

Kristine

CA $119

CA $148 total

includes taxes & fees

Nov 1 - Nov 2

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Stay near popular Southeast Minnesota attractions

Villa Bellezza

8.4/10 (31 reviews)

You can enjoy a tasting or tour at Villa Bellezza during your travels to Pepin. While you're in the area, stroll along the lakeside.

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Mayo Civic Center

9.2/10 (818 reviews)

Catch an event at Mayo Civic Center during your trip to Rochester. Attend a sporting event or simply visit the area's shops.

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Apache Mall

8.6/10 (1,101 reviews)

During your visit to Rochester, you can do some window-shopping at Apache Mall. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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Rochester Recreation Center

8.0/10 (205 reviews)

Catch an event at Rochester Recreation Center during your trip to Rochester. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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National Volleyball Center

7.8/10 (151 reviews)

Catch an event at National Volleyball Center during your trip to Rochester. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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Welch Village Ski Area

8.6/10 (16 reviews)

Hit the slopes in Welch with a visit to Welch Village Ski Area. Stroll along the area's riverfront or simply enjoy its coffeehouses.

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Shattuck-St. Mary's School

9.6/10 (69 reviews)

Enjoy the collegiate vibe when you visit Shattuck-St. Mary's School, during your trip to Faribault. Visit the shops in this family-friendly area, or simply enjoy its coffeehouses.

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Regional Sports Center

8.0/10 (63 reviews)

Catch an event at Regional Sports Center during your trip to Rochester. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

See properties

Learn more about Southeast Minnesota

Explore the family-friendly area of Southeast Minnesota—restaurants, sports teams, and sights from Mayowood Mansion to Apache Mall.

See all hotels in Southeast Minnesota

A lake surrounded by dense forest and a distant hill with a fort.

Top Southeast Minnesota Hotel Reviews

Kahler Inn and Suites - Mayo Clinic Area

8/10 Good

"Convenient Tired, especially the oldest section Parking is a plus but access is a problem for larger vehicles."

Kahler Grand Hotel

10/10 Excellent

"This Hotel has clean rooms with a microwave and small fridge. The front desk staff were pleasant and professional"

AmericInn by Wyndham Rochester Near Mayo Clinic

8/10 Good

"Staff were nice. Room was clean. Close enough to Mayo. Quite a few used shuttle from hotel and said it was very convenient."

EVEN Hotel Rochester - Mayo Clinic Area by IHG

10/10 Excellent

"EVEN is our go-to hotel when visiting Rochester for doctors appointments. It’s close enough to walk and we love the clean modern rooms."

The Plaza Hotel & Suites Winona

10/10 Excellent

"Room was large and comfortable. Great pool and hotter, it was super busy so we did not use it, but it looked fantastic."

Best Western Rochester Hotel Mayo Clinic Area/St. Mary's

8/10 Good

"."

Super 8 by Wyndham Winona MN

8/10 Good

"The property is conveniently located where it's just off of the round-about & close to the grocery store, gas station, Target shopping store, Farm & Fleet, etc. Staff was helpful in getting a room close to the door & a flight of stairs for senior citizen like us with arhritis & special needs. I specially liked the breakfast of coffee, waffle, yogurt, etc. Too bad there's no egg for my protein needs. The bathroom was very clean. I like the body wash, shampoo & conditioner dispensers. However, the table needs a lamp on the table, an ironing board, and some hangers. Other than that, everything's great. We had a comfortable and wonderful stay! Thank you very much. We will come back again!"

Cobblestone Hotel & Suites - Austin

10/10 Excellent

"Clean, front desk was great."

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

3595 Commercial Drive SW Rochester MN

CA $82

CA $94 total

Oct 22 - Oct 23

includes taxes & fees

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $108

CA $119 total

Oct 25 - Oct 26

includes taxes & fees

7.8/10 Good! (1,001 reviews)

Med City Inn & Suites - Mayo Clinic Area

435 16th Ave Nw Rochester MN

CA $106

CA $122 total

Oct 24 - Oct 25

includes taxes & fees

Country Inn & Suites by Radisson, Albert Lea - Austin

2214 E Main St Albert Lea MN

CA $115

CA $127 total

Nov 8 - Nov 9

includes taxes & fees

8.6/10 Excellent! (1,003 reviews)

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $150

CA $166 total

Nov 1 - Nov 2

includes taxes & fees

8.8/10 Excellent! (835 reviews)

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

CA $169

CA $194 total

Oct 23 - Oct 24

includes taxes & fees

Hotels in Southeast Minnesota with star rating

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Book Hotels in Southeast Minnesota on Expedia.com

Find hotels in Southeast Minnesota, MN from CA $94

Change your mind

Treat yourself

Be picky

Go beyond your typical stay in Southeast Minnesota

Check prices for these dates

Filter by

Star rating

Guest rating

Our top choices for Southeast Minnesota hotels

1. EVEN Hotel Rochester - Mayo Clinic Area by IHG

2. Hampton Inn & Suites Rochester-North

3. Hotel Indigo Rochester – Mayo Clinic Area by IHG

4. Econo Lodge Mayo Clinic Area

5. Comfort Inn & Suites Rochester South Mayo Clinic

6. Holiday Inn Express & Suites Rochester – Mayo Clinic Area by IHG

7. AmericInn by Wyndham Rochester Near Mayo Clinic

8. Baymont by Wyndham Kasson Rochester Area

9. Sleep Inn & Suites West-Near Medical Center

10. Spark by Hilton Rochester South

11. Aspen Suites

12. Hyatt House Rochester/Mayo Clinic Area

13. TownePlace Suites by Marriott Rochester

14. Quality Inn & Suites Mayo Clinic Area

15. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

16. Fairfield Inn & Suites Rochester Mayo Clinic Area/St. Marys

17. Home2 Suites by Hilton Rochester Mayo Clinic Area

18. Comfort Inn & Suites West - Medical Center

19. Homewood Suites by Hilton Rochester Mayo Clinic Area / Saint Marys

20. Treasure Island Resort & Casino

Stay near popular Southeast Minnesota attractions

Villa Bellezza

Mayo Civic Center

Apache Mall

Rochester Recreation Center

National Volleyball Center

Welch Village Ski Area

Shattuck-St. Mary's School

Regional Sports Center

Learn more about Southeast Minnesota

Top Southeast Minnesota Hotel Reviews

Kahler Inn and Suites - Mayo Clinic Area

Kahler Grand Hotel

AmericInn by Wyndham Rochester Near Mayo Clinic

EVEN Hotel Rochester - Mayo Clinic Area by IHG

The Plaza Hotel & Suites Winona

Best Western Rochester Hotel Mayo Clinic Area/St. Mary's

Super 8 by Wyndham Winona MN

Cobblestone Hotel & Suites - Austin

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

Boarders Inn & Suites by Cobblestone Hotels - Faribault

Med City Inn & Suites - Mayo Clinic Area

Country Inn & Suites by Radisson, Albert Lea - Austin

Cobblestone Hotel & Suites - Austin

Brentwood Inn & Suites

Hotels in Southeast Minnesota with star rating

Explore a world of travel with Expedia

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