Book The Best Hotels in Southeast Minnesota, MN for 2026 from CA $95 - 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 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 $145

CA $167 total

includes taxes & fees

Oct 4 - Oct 5

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

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

2. Spark by Hilton Rochester South

Rochester

Kimberly

CA $115

CA $132 total

includes taxes & fees

Oct 2 - Oct 3

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 kitchen with a waffle maker, a waffle iron, and a waffle maker instruction manual.

3. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Darlene

CA $109

CA $126 total

includes taxes & fees

Oct 25 - Oct 26

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 bar area with seating and a counter.

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

4. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Kathy

CA $167

CA $192 total

includes taxes & fees

Oct 2 - Oct 3

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

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

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 $146

CA $168 total

includes taxes & fees

Oct 24 - Oct 25

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

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

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

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

6. Comfort Inn & Suites West - Medical Center

Rochester

yuan

CA $126

CA $145 total

includes taxes & fees

Oct 10 - Oct 11

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 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

Jeanne

CA $111

CA $127 total

includes taxes & fees

Sep 27 - Sep 28

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

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.

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

8. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Carrie

CA $153

CA $176 total

includes taxes & fees

Oct 2 - Oct 3

A modern living room with a flat-screen TV, a fireplace, comfortable seating, and a large window with a city view.

A spacious lobby with modern furniture, a spiral staircase, and large windows offering views of the outdoors.

A modern indoor swimming pool with seating areas and a city view.

A modern hotel entrance with a glass facade, illuminated signage, and a covered walkway.

9. Hilton Rochester Mayo Clinic Area

Downtown Rochester

Raymond

CA $254

CA $292 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 interior with a fireplace, a green armchair, and a patterned rug.

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

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

10. Treasure Island Resort & Casino

Welch

Bill

CA $105

CA $133 total

includes taxes & fees

Sep 27 - Sep 28

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.

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

Kutzky Park

Janet

CA $156

CA $179 total

includes taxes & fees

Oct 2 - Oct 3

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

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

12. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

Vickie

CA $173

CA $199 total

includes taxes & fees

Oct 3 - Oct 4

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

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

13. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

Brooke

CA $167

CA $211 total

includes taxes & fees

Oct 24 - Oct 25

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

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

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.

14. TownePlace Suites by Marriott Rochester

Rochester

Terry

CA $139

CA $160 total

includes taxes & fees

Oct 2 - Oct 3

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

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

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.

15. Baymont by Wyndham Kasson Rochester Area

Kasson

Lynnette

CA $94

CA $101 total

includes taxes & fees

Oct 4 - Oct 5

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

A reception area with two counters, a patterned wall, and a wooden floor.

16. Hilton Garden Inn Rochester Downtown, MN

Downtown Rochester

John

CA $161

CA $186 total

includes taxes & fees

Oct 23 - Oct 24

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 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.

17. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $103

CA $118 total

includes taxes & fees

Oct 25 - Oct 26

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

CA $187

CA $215 total

includes taxes & fees

Oct 3 - Oct 4

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.

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

Kutzky Park

Jon

CA $171

CA $196 total

includes taxes & fees

Oct 3 - Oct 4

An indoor swimming pool with clear water, wooden flooring, and a ceiling with wooden beams and lights.

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 room with a TV mounted on the wall, a wooden table, and two patterned armchairs.

20. Med City Inn & Suites - Mayo Clinic Area

Kutzky Park

Rick

CA $101

CA $116 total

includes taxes & fees

Sep 27 - Sep 28

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Vacation Rentals in Southeast Minnesota

Aparthotel

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

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

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

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

The Berkman

Folwell

"Nice property."

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.

Steps to Marina & Beach: Couples Cottage in Pepin

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 marina with boats docked, a parking area, and a view of the surrounding landscape.

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

A bed with a white blanket and patterned pillows, a framed picture on the wall, and a window with a view.

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

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.

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

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

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

Wabasha

"Great property! Very convenient location as well."

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Stay near popular Southeast Minnesota attractions

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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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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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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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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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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Olmsted County Fairgrounds

7.8/10 (177 reviews)

Take the family on an outing to Olmsted County Fairgrounds 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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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

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

8/10 Good

"The hotel is clean, comfortable, and offers easy parking. Mayo Clinic is within walking distance (half mile). The staff is helpful and friendly. Bonus: the pool and hot tub area is very relaxing!"

Kahler Grand Hotel

10/10 Excellent

"Really pleasant stay, has an amazing old charm that feels unique"

Hyatt House Rochester/Mayo Clinic Area

8/10 Good

"Clean rooms. Standard hot breakfast stuff. Liked that they had wheelchairs available. Disliked loud train whistles at 9pm and 5:50am! Also a fair amount of traffic noise could be heard (on 4th floor facing Civic Center Blvd.). Indoor parking lot is small and full at peak times. Had to park 1.5 blocks away."

AmericInn by Wyndham Rochester Near Mayo Clinic

8/10 Good

"Clean room and nice breakfast. Pub on site was a bonus. They had great food."

Express Suites Riverport Inn & Suites

8/10 Good

"The room was clean and the staff was super friendly! Nice variety to choose from in the breakfast! It was a very good experience and I would stay there again!"

La Quinta Inn & Suites by Wyndham Rochester Mayo Clinic S

10/10 Excellent

"Very nice place! I would definitely stay there again."

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

10/10 Excellent

"We had a great night of sleep after a long day at Mayo. The bed was comfortable. Hotel was clean and staff was helpful and very friendly. The breakfast was good with many options."

Kahler Inn and Suites - Mayo Clinic Area

8/10 Good

"Staff at check in,close to mayo"

EVEN Hotel Rochester - Mayo Clinic Area by IHG

10/10 Excellent

"Great breakfast"

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

3595 Commercial Drive SW Rochester MN

CA $82

CA $95 total

Oct 4 - Oct 5

includes taxes & fees

Med City Inn & Suites - Mayo Clinic Area

435 16th Ave Nw Rochester MN

CA $101

CA $116 total

Sep 27 - Sep 28

includes taxes & fees

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $108

CA $119 total

Sep 27 - Sep 28

includes taxes & fees

Country Inn & Suites by Radisson, Albert Lea - Austin

2214 E Main St Albert Lea MN

CA $125

CA $139 total

Oct 18 - Oct 19

includes taxes & fees

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

CA $133

CA $153 total

Oct 1 - Oct 2

includes taxes & fees

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $151

CA $168 total

Oct 1 - Oct 2

includes taxes & fees

Hotels in Southeast Minnesota with star rating

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Rochester Vacations

Book Hotels in Southeast Minnesota on Expedia.com

Find hotels in Southeast Minnesota, MN from CA $95

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. Spark by Hilton Rochester South

3. Comfort Inn & Suites Rochester South Mayo Clinic

4. Hyatt House Rochester/Mayo Clinic Area

5. Hotel Indigo Rochester – Mayo Clinic Area by IHG

6. Comfort Inn & Suites West - Medical Center

7. AmericInn by Wyndham Rochester Near Mayo Clinic

8. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

9. Hilton Rochester Mayo Clinic Area

10. Treasure Island Resort & Casino

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

12. Home2 Suites by Hilton Rochester Mayo Clinic Area

13. EVEN Hotel Rochester - Mayo Clinic Area by IHG

14. TownePlace Suites by Marriott Rochester

15. Baymont by Wyndham Kasson Rochester Area

16. Hilton Garden Inn Rochester Downtown, MN

17. Econo Lodge Mayo Clinic Area

18. Residence Inn by Marriott Rochester Mayo Clinic Area South

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

20. Med City Inn & Suites - Mayo Clinic Area

Vacation Rentals in Southeast Minnesota

The Berkman

Steps to Marina & Beach: Couples Cottage in Pepin

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

Northfield Apt Close to Downtown: Winter Walk

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

Stay near popular Southeast Minnesota attractions

Forestville Mystery Cave State Park

Mayo Civic Center

Apache Mall

National Volleyball Center

Rochester Recreation Center

Welch Village Ski Area

Shattuck-St. Mary's School

Olmsted County Fairgrounds

Learn more about Southeast Minnesota

Top Southeast Minnesota Hotel Reviews

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Kahler Grand Hotel

Hyatt House Rochester/Mayo Clinic Area

AmericInn by Wyndham Rochester Near Mayo Clinic

Express Suites Riverport Inn & Suites

La Quinta Inn & Suites by Wyndham Rochester Mayo Clinic S

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

Kahler Inn and Suites - Mayo Clinic Area

EVEN Hotel Rochester - Mayo Clinic Area by IHG

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

Med City Inn & Suites - Mayo Clinic Area

Boarders Inn & Suites by Cobblestone Hotels - Faribault

Country Inn & Suites by Radisson, Albert Lea - Austin

Brentwood Inn & Suites

Cobblestone Hotel & Suites - Austin

Hotels in Southeast Minnesota with star rating

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