Book The Best Hotels in Southeast Minnesota, MN for 2026 from CA $79 - Fully Refundable Options

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Our top choices for Southeast Minnesota hotels

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 reception desk with a large digital screen displaying a cityscape and the word "happy."

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

1. Hampton Inn & Suites Rochester-North

Rochester

Dr. Tim

CA $139

CA $160 total

includes taxes & fees

Oct 24 - Oct 25

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

A modern interior with a seating area, a bookshelf, and a window with a view of trees.

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

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

2. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

Rici

CA $174

CA $219 total

includes taxes & fees

Oct 23 - Oct 24

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

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 lobby with a central seating area, a reception desk, and a fireplace.

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

3. Comfort Inn & Suites West - Medical Center

Rochester

yuan

CA $121

CA $139 total

includes taxes & fees

Oct 10 - Oct 11

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 laundry area with two Whirlpool washers and a dryer, a wooden shelf above, and a white ceiling.

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

A reception desk with a wooden finish, a large illuminated 'C' sign, and a modern light fixture on the ceiling.

4. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Phil

CA $111

CA $128 total

includes taxes & fees

Nov 1 - Nov 2

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 hotel room with a large bed, a desk, a chair, and a kitchenette.

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

5. Spark by Hilton Rochester South

Rochester

Kimberly

CA $124

CA $142 total

includes taxes & fees

Nov 1 - Nov 2

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.

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

A modern hotel room with a large bed, a sofa, a small table, a desk, and a wardrobe.

6. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

thomas

CA $152

CA $175 total

includes taxes & fees

Oct 23 - Oct 24

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

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

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

A modern reception area with a wooden reception desk, glass pendant lights, and a long hallway with seating.

7. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Van

CA $149

CA $171 total

includes taxes & fees

Oct 24 - Oct 25

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

A modern bar area with seating and a counter.

A modern dining area with round tables and chairs, a large painting on the wall, and a flat-screen TV mounted above a geometric-patterned wall.

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

8. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Kathy

CA $168

CA $193 total

includes taxes & fees

Oct 23 - Oct 24

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

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

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

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

9. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Jeanne

CA $108

CA $124 total

includes taxes & fees

Oct 4 - Oct 5

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

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

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

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

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

Kutzky Park

Janet

CA $174

CA $200 total

includes taxes & fees

Oct 18 - Oct 19

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.

An indoor swimming pool with wooden ceiling beams, yellow chairs, and tables along the sides.

11. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

Vickie

CA $174

CA $200 total

includes taxes & fees

Oct 24 - Oct 25

An indoor swimming pool with slides, seating areas, and a covered section with umbrellas.

A modern kitchen with black cabinets, white countertops, and a tiled backsplash. There are pendant lights, a refrigerator, and a coffee machine.

A hotel room with a kitchen area, a bed, a TV, and a seating area.

A modern kitchen with a microwave, sink, and granite countertop.

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

Rochester

Vicky

CA $135

CA $155 total

includes taxes & fees

Oct 9 - Oct 10

A spacious hotel lobby with multiple seating areas, including sofas and round tables, and a large dining area with yellow chairs.

A spacious lobby with a large seating area, a fireplace, and large windows providing natural light.

A grocery store with refrigerated and frozen sections, shelves stocked with snacks, and a variety of beverages.

A hotel room with a blue sofa, a wooden bench, a small table with a lamp, a painting of a flower, and a kitchenette in the background.

13. Hilton Garden Inn Rochester Downtown, MN

Downtown Rochester

John

CA $162

CA $187 total

includes taxes & fees

Oct 23 - Oct 24

A modern outdoor seating area with a built-in fireplace, two wooden chairs, a table, and a sofa.

A gym with various exercise equipment, including treadmills, stationary bikes, and weight machines.

A hotel room with a kitchenette, a bed, a sofa, a small table, and a window with curtains.

A modern bar area with a long counter, bar stools, and a television screen mounted on the wall.

14. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Sheri

CA $162

CA $190 total

includes taxes & fees

Oct 18 - Oct 19

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

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.

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

15. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $100

CA $115 total

includes taxes & fees

Nov 1 - Nov 2

A modern kitchen with a dark countertop, black cabinets, a microwave, and a refrigerator. There are two pendant lights above the counter.

Two armchairs with striped pillows, a small round table, a clock, and a phone on a counter.

A hotel room with a large round table, two sofas, a TV, and a bed.

A hotel gym with treadmills, elliptical machines, and free weights.

16. Candlewood Suites Rochester Mayo Clinic Area by IHG

Rochester

Sean

CA $165

CA $190 total

includes taxes & fees

Oct 11 - Oct 12

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

A Fairfield Inn & Suites hotel with a modern design, featuring a prominent entrance and a parking area.

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.

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

Kutzky Park

Jon

CA $159

CA $183 total

includes taxes & fees

Oct 17 - Oct 18

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

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

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

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

18. Treasure Island Resort & Casino

Welch

Bill

CA $103

CA $131 total

includes taxes & fees

Oct 26 - Oct 27

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

An outdoor patio area with brick walls, a large arched window, and outdoor seating.

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

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

19. Aspen Suites

Rochester

Dana

CA $212

CA $256 total

includes taxes & fees

Oct 23 - Oct 24

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

A Sleep Inn hotel with a covered entrance, stone pillars, and a clear blue sky.

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

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

20. Sleep Inn & Suites West-Near Medical Center

Rochester

Jacqueline

CA $123

CA $141 total

includes taxes & fees

Oct 11 - Oct 12

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Stay near popular Southeast Minnesota attractions

A cave with a reflective pool and illuminated walls.

Forestville Mystery Cave State Park

9.0/10 (22 reviews)

Commune with nature and explore the great outdoors at Forestville Mystery Cave State Park during your travels in Preston. Wander the parks or discover the area's countryside.

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A courtyard with a stone fountain, yellow buildings with arches, and a clear sky.

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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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

Express Suites Riverport Inn & Suites

8/10 Good

"The property was very good and the staff was very helpful. We enjoyed the stay. We would not hesitate to stay here again."

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

8/10 Good

"Property was clean and smelled fresh. Only complaint is that the a/c was on full blast when I got there and I never could get the heat going. The restaurant (Twigs) and ON CALL shuttle service make this hotel priced right and better than any comparable hotels in the same price range."

Kahler Grand Hotel

10/10 Excellent

"This is a grand hotel - stately, convenient and a delightful place to stay. Loved the walkable "subway" connecting the hotel to restaurants and Mayo Clinic. Enjoyed the Architecture and history of the Plummer Bldg."

Boarders Inn & Suites by Cobblestone Hotels - Faribault

8/10 Good

"It takes a long time for the water to heat up when taking a shower in the morning. The free breakfast had limited items to choose from. Maybe after they finish their renovations it will be better."

AmericInn by Wyndham Rochester Near Mayo Clinic

8/10 Good

"When I tried to call the motels etc by Rochester Mayo. I’d always get Expedia. And we got to go a day early and we still got charged. I thought they had breakfast but my husband said they didn’t. He took our disabled son there.had a nice kitchen nice room pretty clean. Nice staff. Wish it had tubs for adults."

EVEN Hotel Rochester - Mayo Clinic Area by IHG

10/10 Excellent

"Love this hotel! Within close proximity to Mayo Clinic. Very clean, comfortable beds and great amenities. Our number one go to when we stay in Rochester."

Kahler Inn and Suites - Mayo Clinic Area

8/10 Good

"Overall it was a good stay. Pros: this hotel has the underground tunnel connected to the hospital so it was easy walking over, expecially since there is massive construction going on right there. Hotel was clean, staff was wonderful, breakfast was a good variety and good. Rooms were quiet, never heard any of the construction! A detail I may have missed or it wasn’t added in the description was if you parked in there ramp it was 17 dollars a night. Cons: defiantly needs some updating, but biggest con was the room we had was definitely not handicap accessible at all for the bathroom. Being “connect” to the hospital and the amount of the elderly I would think it would have something there. Toilet was so low almost ment for a child, and extremely tiny room, no grab bars, and step in shower/tub. I would stay here again, most definitely but not if I had elderly with me again"

Brentwood Inn & Suites

10/10 Excellent

"Staff was very helpful and kind. Desk chair worn and could use a replacement-normally would not care but was working remote while there. Wi-Fi great"

La Quinta Inn & Suites by Wyndham Rochester Mayo Clinic S

10/10 Excellent

"The employees are very helpful in every way possible"

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

3595 Commercial Drive SW Rochester MN

CA $83

CA $95 total

Oct 5 - Oct 6

includes taxes & fees

7.6/10 Good! (87 reviews)

Med City Inn & Suites - Mayo Clinic Area

435 16th Ave Nw Rochester MN

CA $102

CA $117 total

Oct 4 - Oct 5

includes taxes & fees

7.8/10 Good! (1,027 reviews)

Country Inn & Suites by Radisson, Albert Lea - Austin

2214 E Main St Albert Lea MN

CA $109

CA $120 total

Nov 1 - Nov 2

includes taxes & fees

8.6/10 Excellent! (1,001 reviews)

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $109

CA $121 total

Oct 6 - Oct 7

includes taxes & fees

7.8/10 Good! (1,000 reviews)

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

CA $134

CA $154 total

Oct 29 - Oct 30

includes taxes & fees

8.8/10 Excellent! (1,005 reviews)

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $152

CA $169 total

Oct 11 - Oct 12

includes taxes & fees

Hotels in Southeast Minnesota with star rating

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Find hotels in Southeast Minnesota, MN from CA $79

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. Hampton Inn & Suites Rochester-North

2. EVEN Hotel Rochester - Mayo Clinic Area by IHG

3. Comfort Inn & Suites West - Medical Center

4. Comfort Inn & Suites Rochester South Mayo Clinic

5. Spark by Hilton Rochester South

6. Hotel Indigo Rochester – Mayo Clinic Area by IHG

7. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

8. Hyatt House Rochester/Mayo Clinic Area

9. AmericInn by Wyndham Rochester Near Mayo Clinic

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

11. Home2 Suites by Hilton Rochester Mayo Clinic Area

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

13. Hilton Garden Inn Rochester Downtown, MN

14. Staybridge Suites Rochester - Mayo Clinic Area by IHG

15. Econo Lodge Mayo Clinic Area

16. Candlewood Suites Rochester Mayo Clinic Area by IHG

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

18. Treasure Island Resort & Casino

19. Aspen Suites

20. Sleep Inn & Suites West-Near Medical Center

Stay near popular Southeast Minnesota attractions

Forestville Mystery Cave State Park

Villa Bellezza

Mayo Civic Center

Apache Mall

Rochester Recreation Center

National Volleyball Center

Welch Village Ski Area

Shattuck-St. Mary's School

Learn more about Southeast Minnesota

Top Southeast Minnesota Hotel Reviews

Express Suites Riverport Inn & Suites

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Kahler Grand Hotel

Boarders Inn & Suites by Cobblestone Hotels - Faribault

AmericInn by Wyndham Rochester Near Mayo Clinic

EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kahler Inn and Suites - Mayo Clinic Area

Brentwood Inn & Suites

La Quinta Inn & Suites by Wyndham Rochester Mayo Clinic S

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

Med City Inn & Suites - Mayo Clinic Area

Country Inn & Suites by Radisson, Albert Lea - Austin

Boarders Inn & Suites by Cobblestone Hotels - Faribault

Brentwood Inn & Suites

Cobblestone Hotel & Suites - Austin

Hotels in Southeast Minnesota with star rating

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