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

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."

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 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.

2. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

Rici

CA $174

CA $219 total

includes taxes & fees

Oct 24 - Oct 25

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 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.

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

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

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

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

4. Spark by Hilton Rochester South

Rochester

Kimberly

CA $124

CA $142 total

includes taxes & fees

Nov 2 - Nov 3

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

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

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

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

5. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

thomas

CA $152

CA $175 total

includes taxes & fees

Oct 24 - Oct 25

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.

6. Comfort Inn & Suites West - Medical Center

Rochester

yuan

CA $120

CA $139 total

includes taxes & fees

Oct 10 - Oct 11

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

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.

A modern bar area with seating and a counter.

7. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Kathy

CA $168

CA $193 total

includes taxes & fees

Oct 17 - Oct 18

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

8. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Van

CA $148

CA $171 total

includes taxes & fees

Oct 10 - Oct 11

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

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.

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

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

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.

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

10. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

Vickie

CA $174

CA $200 total

includes taxes & fees

Oct 24 - Oct 25

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

11. Aspen Suites

Rochester

Dana

CA $202

CA $244 total

includes taxes & fees

Oct 3 - Oct 4

A room with a fireplace, two leather armchairs, a sofa, and a large window providing a view of the outdoors.

A paved garden area with two benches, a potted plant with yellow flowers, and a variety of greenery.

A long, narrow hotel corridor with a carpeted floor, light fixtures along the walls, and a ceiling with recessed lighting.

A reception area with a curved counter, ceiling lights, and a potted plant.

12. Brentwood Inn & Suites

Downtown Rochester

Daniel

CA $133

CA $154 total

includes taxes & fees

Oct 29 - Oct 30

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

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.

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

13. Hilton Garden Inn Rochester Downtown, MN

Downtown Rochester

John

CA $162

CA $187 total

includes taxes & fees

Oct 24 - Oct 25

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.

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

Kutzky Park

Janet

CA $162

CA $187 total

includes taxes & fees

Oct 10 - Oct 11

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

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.

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

15. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Sheri

CA $152

CA $178 total

includes taxes & fees

Nov 1 - Nov 2

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

A bar with wooden stools and a neon sign.

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.

16. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Jeanne

CA $108

CA $124 total

includes taxes & fees

Oct 4 - Oct 5

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

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.

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

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

Rochester

Vicky

CA $135

CA $155 total

includes taxes & fees

Oct 10 - Oct 11

A coffee shop interior with a wooden counter, menu boards, and seating area.

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

An outdoor seating area with tables and chairs, a neon sign, and flower arrangements.

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

18. TownePlace Suites by Marriott Rochester Mayo Clinic Area

Kutzky Park

Hafsa

CA $195

CA $224 total

includes taxes & fees

Oct 17 - Oct 18

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

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.

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

19. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $100

CA $115 total

includes taxes & fees

Nov 1 - Nov 2

An indoor swimming pool with a wooden ceiling, clear blue water, and seating areas around the pool.

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

A café with multiple tables and chairs, a kitchen area with appliances, and a clock on the wall.

A coffee station with a coffee machine, cups, and a Bigelow tea display.

20. Med City Inn & Suites - Mayo Clinic Area

Kutzky Park

Rick

CA $102

CA $117 total

includes taxes & fees

Oct 3 - Oct 4

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Vacation Rentals in Southeast Minnesota

Aparthotel

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

A modern pool table in a spacious, well-lit room with large windows and a bar area.

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

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.

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

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

Broadway Plaza, Trademark Collection by Wyndham

Downtown Rochester

"As always excellent staff, clean and comfortable rooms. Great central location. "

Apartment

A two-story building with a green exterior, a covered porch, and a driveway leading to a garage.

A cozy room with a sofa bed, a small side table, and a window with blinds.

A room with a large window, a flat-screen TV mounted on the wall, a fluffy chair, a small round table, and a chair with a basket.

A modern kitchen with stainless steel appliances, wooden cabinets, and a dishwasher.

Northfield Apt Close to Downtown: Winter Walk

Northfield

"It was amazing!"

Apartment

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

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

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.

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

A kitchen with wooden cabinets, a stove, a sink, and a window with a view of trees.

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

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

Treasure Island Resort & Casino

10/10 Excellent

"We stayed in the Buffalo Tower which had recently been renovated. Our room was a double Queen. It was spacious along with the bathroom. A pleasant stay with a secure atmosphere as there was an attendant by the elevators and you needed your room key card to summon the elevator. We ate a number of times at "Currents" located in the Property. The food and service was very good. Definitely an impressive property."

Aspen Select

10/10 Excellent

"access to the property"

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"

Express Suites Riverport Inn & Suites

10/10 Excellent

"We alway stay at Riverport when in Winona! Staff is kind and the breakfast is great! And it’s in close proximity to campus!"

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"

Kahler Grand Hotel

10/10 Excellent

"Perfect for the outpatient setting for Mayo. Definitely recommend using valet for just a little more it’s worth it and so easy!"

La Quinta Inn & Suites by Wyndham Rochester Mayo Clinic S

10/10 Excellent

"The employees are very helpful in every way possible"

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

10/10 Excellent

"there staff supper nice, i will come back"

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 3 - Oct 4

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! (1,009 reviews)

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

CA $133

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 12 - Oct 13

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 Rochester South Mayo Clinic

4. Spark by Hilton Rochester South

5. Hotel Indigo Rochester – Mayo Clinic Area by IHG

6. Comfort Inn & Suites West - Medical Center

7. Hyatt House Rochester/Mayo Clinic Area

8. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

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

10. Home2 Suites by Hilton Rochester Mayo Clinic Area

11. Aspen Suites

12. Brentwood Inn & Suites

13. Hilton Garden Inn Rochester Downtown, MN

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

15. Staybridge Suites Rochester - Mayo Clinic Area by IHG

16. AmericInn by Wyndham Rochester Near Mayo Clinic

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

18. TownePlace Suites by Marriott Rochester Mayo Clinic Area

19. Econo Lodge Mayo Clinic Area

20. Med City Inn & Suites - Mayo Clinic Area

Vacation Rentals in Southeast Minnesota

The Berkman

Broadway Plaza, Trademark Collection by Wyndham

Northfield Apt Close to Downtown: Winter Walk

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

Pet-friendly Cabin Retreat: Walk to Lake Pepin!

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

Treasure Island Resort & Casino

Aspen Select

EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kahler Inn and Suites - Mayo Clinic Area

Express Suites Riverport Inn & Suites

Brentwood Inn & Suites

Kahler Grand Hotel

La Quinta Inn & Suites by Wyndham Rochester Mayo Clinic S

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

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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