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

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

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

1. Hampton Inn & Suites Rochester-North

Rochester

Dr. Tim

CA $145

CA $167 total

includes taxes & fees

Oct 4 - Oct 5

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

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

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.

2. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Kathy

CA $167

CA $192 total

includes taxes & fees

Oct 23 - Oct 24

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

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

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.

3. Comfort Inn & Suites West - Medical Center

Rochester

yuan

CA $126

CA $145 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 snack bar with a variety of packaged snacks, a refrigerator stocked with beverages, and a microwave.

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

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

4. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Darlene

CA $122

CA $140 total

includes taxes & fees

Oct 26 - Oct 27

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".

5. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

Brooke

CA $173

CA $218 total

includes taxes & fees

Oct 2 - Oct 3

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 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.

6. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Carrie

CA $147

CA $170 total

includes taxes & fees

Oct 24 - Oct 25

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.

7. Spark by Hilton Rochester South

Rochester

Kimberly

CA $115

CA $132 total

includes taxes & fees

Oct 4 - Oct 5

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 hotel room with a bed, desk, and kitchenette.

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

8. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

Vickie

CA $173

CA $199 total

includes taxes & fees

Oct 24 - Oct 25

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

A modern hotel lobby with a curved staircase, seating areas, and large windows.

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

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

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 slides, seating areas, and a covered section with umbrellas.

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

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.

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

Rochester

Vicky

CA $140

CA $161 total

includes taxes & fees

Oct 1 - Oct 2

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.

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

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

11. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

thomas

CA $151

CA $174 total

includes taxes & fees

Oct 24 - Oct 25

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.

A bar with wooden stools and a neon sign.

12. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Jeanne

CA $115

CA $132 total

includes taxes & fees

Sep 30 - Oct 1

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

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.

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

Kutzky Park

Janet

CA $156

CA $179 total

includes taxes & fees

Oct 3 - Oct 4

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

14. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $103

CA $118 total

includes taxes & fees

Oct 25 - Oct 26

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

A Microtel Inn & Suites building with a signboard, a parking lot, and a clear sky.

A reception area with a reception desk, two armchairs, a clock, and a framed artwork on the wall.

A compact hotel room with a kitchenette, a dining area, a sofa, and a bed.

15. Microtel Inn & Suites by Wyndham Rochester North Mayo Clinic

Rochester

Richard

CA $99

CA $113 total

includes taxes & fees

Sep 29 - Sep 30

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

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.

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

16. Aspen Suites

Rochester

Dana

CA $200

CA $242 total

includes taxes & fees

Oct 2 - Oct 3

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

17. Treasure Island Resort & Casino

Welch

Bill

CA $103

CA $130 total

includes taxes & fees

Sep 29 - Sep 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.

18. Hilton Garden Inn Rochester Downtown, MN

Downtown Rochester

John

CA $161

CA $186 total

includes taxes & fees

Oct 23 - Oct 24

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

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

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

19. TownePlace Suites by Marriott Rochester Mayo Clinic Area

Kutzky Park

Hafsa

CA $194

CA $223 total

includes taxes & fees

Oct 2 - Oct 3

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

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.

A gym with treadmills, an elliptical, and a water station.

20. Med City Inn & Suites - Mayo Clinic Area

Kutzky Park

Rick

CA $101

CA $116 total

includes taxes & fees

Sep 28 - Sep 29

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Vacation 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.

A modern pool table in a spacious, well-lit room with large windows and a bar 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 wooden cabin interior with a bed, a ceiling light, and a window.

A modern kitchen with stainless steel appliances, wooden cabinets, and a stone tile floor.

Steps to Marina & Beach: Couples Cottage in Pepin

Pepin

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

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 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 deck with two wooden chairs and a fire pit.

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

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

Lake City

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

Cottage

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

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

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.

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!"

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 kitchen with wooden cabinets, stainless steel appliances, and a dining table with chairs.

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."

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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

AmericInn by Wyndham Rochester Near Mayo Clinic

8/10 Good

"Great price, my child enjoyed the pool area, room was comfortable, staff was great!"

Med City Inn & Suites - Mayo Clinic Area

8/10 Good

"Quiet and comfortable."

Brentwood Inn & Suites

10/10 Excellent

"Got in pretty late, but the front desk staff were very friendly and accommodating. My room was clean, bed was very comfortable. I also enjoyed the continental breakfast and coffee in the morning."

Kahler Grand Hotel

10/10 Excellent

"Staff very helpful. Essex restaurant very good. Rooms small. Overall good."

Hyatt House Rochester/Mayo Clinic Area

10/10 Excellent

"Na"

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!"

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."

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 28 - Sep 29

includes taxes & fees

7.8/10 Good! (1,026 reviews)

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $108

CA $119 total

Sep 29 - Sep 30

includes taxes & fees

Country Inn & Suites by Radisson, Albert Lea - Austin

2214 E Main St Albert Lea MN

CA $115

CA $128 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

8.8/10 Excellent! (1,006 reviews)

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $151

CA $168 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 $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. Hyatt House Rochester/Mayo Clinic Area

3. Comfort Inn & Suites West - Medical Center

4. Comfort Inn & Suites Rochester South Mayo Clinic

5. EVEN Hotel Rochester - Mayo Clinic Area by IHG

6. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

7. Spark by Hilton Rochester South

8. Home2 Suites by Hilton Rochester Mayo Clinic Area

9. Hilton Rochester Mayo Clinic Area

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

11. Hotel Indigo Rochester – Mayo Clinic Area by IHG

12. AmericInn by Wyndham Rochester Near Mayo Clinic

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

14. Econo Lodge Mayo Clinic Area

15. Microtel Inn & Suites by Wyndham Rochester North Mayo Clinic

16. Aspen Suites

17. Treasure Island Resort & Casino

18. Hilton Garden Inn Rochester Downtown, MN

19. TownePlace Suites by Marriott Rochester Mayo Clinic Area

20. Med City Inn & Suites - Mayo Clinic Area

Vacation Rentals in Southeast Minnesota

The Berkman

Steps to Marina & Beach: Couples Cottage in Pepin

Northfield Apt Close to Downtown: Winter Walk

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

Pet-friendly Cabin Retreat: Walk to Lake Pepin!

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

AmericInn by Wyndham Rochester Near Mayo Clinic

Med City Inn & Suites - Mayo Clinic Area

Brentwood Inn & Suites

Kahler Grand Hotel

Hyatt House Rochester/Mayo Clinic Area

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

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

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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