Best Southeast Minnesota Hotels in 2026 from HK$433 - Fully Refundable Options

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Our top choices for Southeast Minnesota hotels

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 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 bar area with seating and a counter.

1. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Arlan

HK$996

HK$1,147 total

includes taxes & fees

13 Nov - 14 Nov

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

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

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

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

HK$804

HK$925 total

includes taxes & fees

6 Nov - 7 Nov

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

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

3. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

James

HK$863

HK$1,099 total

includes taxes & fees

6 Nov - 7 Nov

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

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

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

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

4. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

howard

HK$860

HK$990 total

includes taxes & fees

7 Nov - 8 Nov

A modern kitchen with a central island, wooden cabinets, and pendant lighting.

A hotel exterior with a 'Townplace Suites' sign, outdoor seating area, and 'OPEN' signage.

A hotel room with a bed, bedside table, and a window with curtains.

5. TownePlace Suites by Marriott Rochester Mayo Clinic Area

Kutzky Park

Cory

HK$1,074

HK$1,237 total

includes taxes & fees

6 Nov - 7 Nov

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.

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

Kutzky Park

Brien

HK$911

HK$1,048 total

includes taxes & fees

6 Nov - 7 Nov

A modern interior with a bar area, seating, and a large window.

A spacious outdoor dining area with multiple tables and chairs, large windows, and a wooden ceiling structure.

A modern hotel building with a prominent sign for 'Hotel Indigo' and a 'Crave Drink' establishment.

A bar area with a central island, bar stools, and hanging pendant lights.

7. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

Naomi

HK$776

HK$894 total

includes taxes & fees

26 Nov - 27 Nov

A modern living room with a fireplace, comfortable seating, and large windows.

A modern interior with a seating area, a bookshelf, and a view through large windows.

A modern hotel entrance with a glass facade, a staircase leading to the entrance, and a sign for Staybridge Suites.

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

8. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Amanda

HK$823

HK$964 total

includes taxes & fees

25 Nov - 26 Nov

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

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

9. Comfort Inn & Suites West - Medical Center

Rochester

Tammy

HK$677

HK$779 total

includes taxes & fees

15 Nov - 16 Nov

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

A gym with exercise equipment, a clock, and a window with blinds.

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

A conference room with tables set for a meeting, a projector screen, and a view of the outside.

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

Kutzky Park

Lin

HK$860

HK$990 total

includes taxes & fees

25 Nov - 26 Nov

A modern hotel lobby with multiple seating areas, including a central dining table with chairs, a bar area, and a seating section with cushioned chairs.

A modern lounge area with a curved sofa, a round table, and a seating area with chairs.

A modern conference room with a long table, multiple chairs, and a wooden partition.

A modern hotel room with a large bed, two bedside tables, and built-in lighting.

11. SpringHill Suites by Marriott Rochester-Mayo Clinic/St Marys

Kutzky Park

Jackie

HK$875

HK$1,008 total

includes taxes & fees

1 Nov - 2 Nov

A swimming pool with a glass ceiling, a neon sign for the KAFFLER HOTEL, and a view of the city skyline at dusk.

A hotel room with a large bed, a desk, a chair, a microwave, and a framed picture on the wall.

A hotel entrance with a modern design, large windows, and a sign indicating it's a Grand Hotel.

A banquet hall with round tables, chairs, chandeliers, and a fireplace.

12. Kahler Grand Hotel

Downtown Rochester

Christina

HK$1,152

HK$1,326 total

includes taxes & fees

28 Oct - 29 Oct

A modern living room with a flat-screen TV, a fireplace, a sofa, a coffee table, and a view of a cityscape through large windows.

A spacious lobby with modern furniture, a staircase, and large windows.

A hotel swimming pool with lounge chairs, a changing room, and a view of the cityscape.

A spacious lobby with a curved staircase, comfortable seating areas, and large windows offering views of the outdoors.

13. Hilton Rochester Mayo Clinic Area

Downtown Rochester

Jennifer

HK$1,393

HK$1,604 total

includes taxes & fees

7 Nov - 8 Nov

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.

14. Sleep Inn & Suites West-Near Medical Center

Rochester

Jacqueline

HK$600

HK$690 total

includes taxes & fees

15 Nov - 16 Nov

A Comfort Inn & Suites hotel with a modern design, featuring a prominent signage and a parking lot.

A hotel room with a bed, a desk, a chair, a sofa, and artwork on the walls.

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

A modern living room with a sofa, two armchairs, a coffee table, and a large window offering a view of the outdoors.

15. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Terri

HK$589

HK$678 total

includes taxes & fees

7 Nov - 8 Nov

A reception area with a wooden reception desk, a "Welcome to the Bread & Butter State" sign, and a "Please Center" sign.

A pool area with a table and chairs, a lifeguard chair, and a pool lift.

A modern lounge area with seating arrangements, a reception desk, and a patterned wall.

A hotel room with a bed, a desk, a chair, a TV, and a bathroom visible through an open door.

16. Hampton Inn Rochester-South

Rochester

Susan

HK$767

HK$883 total

includes taxes & fees

1 Nov - 2 Nov

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

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

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.

17. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Deanna

HK$896

HK$1,031 total

includes taxes & fees

31 Oct - 1 Nov

A swimming pool with clear blue water, surrounded by lounge chairs and a view of residential buildings through large windows.

A modern reception area with a brick-patterned wall, two reception desks, a flat-screen TV, and seating arrangements including a sofa and chairs.

A modern lounge area with seating, a fireplace, and a bar area.

A modern hotel with a flat roof, multiple windows, and a covered outdoor seating area.

18. Residence Inn by Marriott Rochester Mayo Clinic Area South

Rochester

Chee

HK$1,035

HK$1,192 total

includes taxes & fees

13 Nov - 14 Nov

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

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

A hotel lobby with leather sofas, a stone fireplace, and a patterned carpet.

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

19. Econo Lodge Mayo Clinic Area

Rochester

Ashley

HK$514

HK$592 total

includes taxes & fees

15 Nov - 16 Nov

A Staybridge Suites hotel with a stone facade, a covered entrance, and multiple windows.

An indoor swimming pool with clear water, surrounded by lounge chairs and a sunbed.

A hotel lobby with a fireplace, seating area, and a bar.

A modern kitchen with dark wood cabinets, stainless steel appliances, and a central island with seating.

20. Staybridge Suites Rochester - Commerce Dr NW by IHG

Rochester

MATTHEW

HK$910

HK$1,047 total

includes taxes & fees

7 Nov - 8 Nov

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Holiday Rentals in Southeast Minnesota

Aparthotel

A spacious living area with a modern staircase, leather sofas, and contemporary lighting.

A rooftop pool area with lounge chairs and umbrellas, surrounded by a modern building with a brick facade.

A modern interior with a large dining table, sofas, and a kitchen area.

An outdoor seating area with blue sofas and wicker chairs, a wooden table, and green ottomans on a tiled patio.

The Berkman

Folwell

"Excellent service and wonderful room!"

Apartment

A bedroom with a large bed, a TV on a dresser, and a view of the city through large windows.

A multi-story building with the sign 'Broadway Plaza' indicating a commercial or hotel property.

An indoor swimming pool with a clock on the wall, lounge chairs, and a lifeguard warning sign.

Broadway Plaza, Trademark Collection by Wyndham

Downtown Rochester

"Clean room and great location"

Apartment

A wooden interior with a kitchen, bar area, and a staircase.

A two-story building with a storefront featuring a sign for coffee, ice cream, and craft drinks. There are steps leading to the entrance, a bench outside, and potted plants.

A cafe with outdoor seating, a large tree, and a view of the water.

A wooden cabin interior with a bed, a ceiling light, and a window.

Lake Pepin Escape: Loft Cottage & Fireplace

Pepin

"Great location and very well furnished with new appliances."

Apartment

A modern kitchen with a central island, bar stools, and a large window.

A spacious living area with a large sofa, a coffee table, and a dining table with chairs. There is a ceiling fan and a floor lamp.

A spacious living room with a large sofa set, a wooden coffee table, and a large window.

A deck with two wooden chairs and a fire pit.

1 Block to Lake City Marina: Condo w/ Rooftop Deck

Lake City

"Wonderful property, spacious, well-appointed and comfortable. Would definitely rent again."

Apartment

A bedroom with a bed, a chair, a table, a fireplace, and a ceiling fan.

A single-story house with a front porch, a small staircase leading to a deck, and a stone retaining wall.

A living room with a fireplace, a television mounted above it, and a large window offering a view of the outdoors.

A wooden deck with Adirondack chairs lined up against a building with a flag.

Pet-friendly Wabasha Studio: Boat, Ski & Explore!

Wabasha

"Great property! Very convenient location as well."

Cottage

A modern interior with a stone fireplace, wooden walls, a leather sofa, and a dining area.

A log cabin interior with a wooden ceiling, a red sofa, a brown leather couch, and a person seated on a chair.

A bedroom with a wooden bed, a desk, a lamp, and large windows with a view of trees.

A cozy interior with a wooden ceiling, a fireplace, a red sofa, a leather couch, and a foosball table.

Pet-friendly Cabin Retreat: Walk to Lake Pepin!

Pepin

"What a fun place! Plenty of room. We played foosball had a fire outside. We enjoyed the fireplace too. We hadn’t anticipated no TV though. You might want to add that to your description. The water is definitely smelly, so we truly appreciated the 40 bottles of water you provided. Definitely a great place for a girl’s weekend or family reunion!"

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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 find the perfect gifts to bring home 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 cafes.

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Shattuck-St. Mary's School

9.6/10 (69 reviews)

Explore the campus of Shattuck-St. Mary's School during your trip to Faribault. Visit the shops in this family-friendly area or simply enjoy its cafes.

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Mayowood Mansion

9.4/10 (29 reviews)

You can spend time studying the exhibits at Mayowood Mansion in Rochester. Attend a sporting event or simply enjoy the top-notch restaurants while you're in the area.

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Learn more about Southeast Minnesota

Discover the family-friendly area of Southeast Minnesota—sports teams, a scenic riverfront 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

Hyatt House Rochester/Mayo Clinic Area

10/10 Excellent

"Room was clean, building well maintained. Staff friendly and helpful."

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

8/10 Good

"Comfortable place. Nice patio that allows pets."

Cobblestone Hotel & Suites - Austin

8/10 Good

"We chose this hotel because it had a bar. I wanted to take a glass of wine back to my room. What a disappointment! There was one bottle of very bad of red and a warm Chardonnay. Okay I’ll have a gin and tonic. Nope. No tonic. The receptionist doubled a bartender. She did her best but didn’t have much to work with"

AmericInn by Wyndham Rochester Near Mayo Clinic

8/10 Good

"The room had some noise like water going thru some pipes during the early morning hours. Could be something due to the swimming pool. No sleep after that started."

Hotel Indigo Rochester – Mayo Clinic Area by IHG

10/10 Excellent

"Staff was extremely helpful and knowledgeable. Restaurant was clean and food was great. Very close to everything and parking was easy and inexpensive."

Brentwood Inn & Suites

8/10 Good

"While the property is old, I found it very clean. Location is excellent. Bed was not great. Staff was incredibly accommodating."

More cheap stays in Southeast Minnesota

Super 8 by Wyndham Winona MN

1025 Sugar Loaf Rd Winona MN

HK$381

HK$433 total

15 Nov - 16 Nov

includes taxes & fees

Quality Inn near Medical Center

5708 Bandel Road NW Rochester MN

HK$493

HK$568 total

15 Nov - 16 Nov

includes taxes & fees

Med City Inn & Suites - Mayo Clinic Area

435 16th Ave Nw Rochester MN

HK$593

HK$683 total

27 Oct - 28 Oct

includes taxes & fees

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

1517 16th St Sw Rochester MN

HK$778

HK$896 total

1 Nov - 2 Nov

includes taxes & fees

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

HK$840

HK$931 total

27 Oct - 28 Oct

includes taxes & fees

8.8/10 Excellent! (836 reviews)

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

HK$941

HK$1,083 total

29 Oct - 30 Oct

includes taxes & fees

8.8/10 Excellent! (1,005 reviews)

Southeast Minnesota hotels from HK$433

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. Hyatt House Rochester/Mayo Clinic Area

2. Hampton Inn & Suites Rochester-North

3. EVEN Hotel Rochester - Mayo Clinic Area by IHG

4. Home2 Suites by Hilton Rochester Mayo Clinic Area

5. TownePlace Suites by Marriott Rochester Mayo Clinic Area

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

7. Hotel Indigo Rochester – Mayo Clinic Area by IHG

8. Staybridge Suites Rochester - Mayo Clinic Area by IHG

9. Comfort Inn & Suites West - Medical Center

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

11. SpringHill Suites by Marriott Rochester-Mayo Clinic/St Marys

12. Kahler Grand Hotel

13. Hilton Rochester Mayo Clinic Area

14. Sleep Inn & Suites West-Near Medical Center

15. Comfort Inn & Suites Rochester South Mayo Clinic

16. Hampton Inn Rochester-South

17. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

18. Residence Inn by Marriott Rochester Mayo Clinic Area South

19. Econo Lodge Mayo Clinic Area

20. Staybridge Suites Rochester - Commerce Dr NW by IHG

Holiday Rentals in Southeast Minnesota

The Berkman

Broadway Plaza, Trademark Collection by Wyndham

Lake Pepin Escape: Loft Cottage & Fireplace

1 Block to Lake City Marina: Condo w/ Rooftop Deck

Pet-friendly Wabasha Studio: Boat, Ski & Explore!

Pet-friendly Cabin Retreat: Walk to Lake Pepin!

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

Mayowood Mansion

Learn more about Southeast Minnesota

Top Southeast Minnesota Hotel Reviews

Hyatt House Rochester/Mayo Clinic Area

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Cobblestone Hotel & Suites - Austin

AmericInn by Wyndham Rochester Near Mayo Clinic

Hotel Indigo Rochester – Mayo Clinic Area by IHG

Brentwood Inn & Suites

More cheap stays in Southeast Minnesota

Super 8 by Wyndham Winona MN

Quality Inn near Medical Center

Med City Inn & Suites - Mayo Clinic Area

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

Cobblestone Hotel & Suites - Austin

Brentwood Inn & Suites

Hotels in Southeast Minnesota with star-rating

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