Book The Best Hotels in Southeast Minnesota, MN for 2026 from CA $80 - 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 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 hotel room with a large bed, a desk with a chair, a window with a view of the outdoors, and two bedside lamps.

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

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.

2. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Phil

CA $123

CA $142 total

includes taxes & fees

Oct 10 - Oct 11

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

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.

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

Rici

CA $168

CA $213 total

includes taxes & fees

Nov 6 - Nov 7

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

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

4. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

thomas

CA $152

CA $176 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 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 Hyatt House hotel with a prominent 'Hyatt House' sign, multiple floors, and a parking garage.

5. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Kathy

CA $168

CA $194 total

includes taxes & fees

Oct 17 - Oct 18

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

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.

An indoor swimming pool with wooden beams and white chairs around it.

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

6. Baymont by Wyndham Kasson Rochester Area

Kasson

Lynnette

CA $92

CA $99 total

includes taxes & fees

Oct 18 - Oct 19

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

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.

7. Hilton Garden Inn Rochester Downtown, MN

Downtown Rochester

Richard

CA $162

CA $187 total

includes taxes & fees

Oct 23 - Oct 24

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 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.

8. Treasure Island Resort & Casino

Welch

Bill

CA $104

CA $131 total

includes taxes & fees

Oct 26 - Oct 27

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.

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

Rochester

Vicky

CA $135

CA $155 total

includes taxes & fees

Oct 10 - Oct 11

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.

10. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

Vickie

CA $174

CA $200 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 hotel room with a large bed, a desk, a chair, and a kitchenette.

11. Spark by Hilton Rochester South

Rochester

Stanton

CA $121

CA $139 total

includes taxes & fees

Oct 12 - Oct 13

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

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

12. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Christina

CA $145

CA $167 total

includes taxes & fees

Oct 24 - Oct 25

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.

13. Candlewood Suites Rochester Mayo Clinic Area by IHG

Rochester

Sean

CA $165

CA $190 total

includes taxes & fees

Oct 9 - Oct 10

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

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.

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

14. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $100

CA $115 total

includes taxes & fees

Nov 1 - Nov 2

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.

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

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

15. Aspen Suites

Rochester

Dana

CA $191

CA $231 total

includes taxes & fees

Oct 23 - Oct 24

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

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

Kutzky Park

Janet

CA $157

CA $181 total

includes taxes & fees

Nov 6 - Nov 7

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 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

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.

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

A bar with wooden stools and a neon sign.

18. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Jeanne

CA $104

CA $120 total

includes taxes & fees

Oct 25 - Oct 26

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

A modern kitchen with a central island, bar stools, and pendant lighting. A living area with a sofa, ottoman, and a view of the outdoors is visible.

A modern urban street with tall buildings, a pedestrian walkway, and a parking area.

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

19. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Sheri

CA $152

CA $178 total

includes taxes & fees

Oct 18 - Oct 19

A Courtyard Marriott hotel with multiple floors, a brick facade, and illuminated signage.

A modern living room with a sofa, a round coffee table, and a side table. There are large windows with a view of the outside.

A hotel room with a sofa, armchairs, a small kitchenette, a flat-screen TV, and a large window.

A hotel room with a bed, a sofa, a desk, a TV, and a wall art piece.

20. Courtyard by Marriott Rochester Mayo Clinic Area/Saint Marys

Kutzky Park

MATTHEW

CA $175

CA $201 total

includes taxes & fees

Oct 10 - Oct 11

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

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

"The staff were friendly and very helpful when we had questions. The kitchen was well equipped and clean. The parking was handy and lived the Skywalks."

Apartment

A rustic kitchen with wooden bar stools, a stainless steel refrigerator, and a wooden island with a sink.

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

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

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

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.

Downtown Northfield Apt: Winter Walk & Shops

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 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.

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

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

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 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."

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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

EVEN Hotel Rochester - Mayo Clinic Area by IHG

10/10 Excellent

"good"

St James Hotel, a Historic Hotel of America

10/10 Excellent

"Cool place"

Express Suites Riverport Inn & Suites

8/10 Good

"The screen on our deck door was ripped, which would let bugs in. Probably our only complaint"

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

8/10 Good

"Excellent location. Great shuttle service to mayo gonna. No working wifi in my room but other than that was fine."

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

10/10 Excellent

"We had a very nice stay. We were able to Walk to Mayo and enjoyed the attached Twigs restaurant."

Cobblestone Hotel & Suites - Austin

10/10 Excellent

"Everything was ok plus breakfast is included"

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"

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

3595 Commercial Drive SW Rochester MN

CA $83

CA $95 total

Oct 7 - Oct 8

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 7 - Oct 8

includes taxes & fees

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $110

CA $121 total

Oct 19 - Oct 20

includes taxes & fees

7.8/10 Good! (1,001 reviews)

Country Inn & Suites by Radisson, Albert Lea - Austin

2214 E Main St Albert Lea MN

CA $114

CA $126 total

Nov 1 - Nov 2

includes taxes & fees

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 $153

CA $169 total

Oct 11 - Oct 12

includes taxes & fees

8.8/10 Excellent! (822 reviews)

Hotels in Southeast Minnesota with star rating

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Book Hotels in Southeast Minnesota on Expedia.com

Find hotels in Southeast Minnesota, MN from CA $80

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. Comfort Inn & Suites Rochester South Mayo Clinic

3. EVEN Hotel Rochester - Mayo Clinic Area by IHG

4. Hotel Indigo Rochester – Mayo Clinic Area by IHG

5. Hyatt House Rochester/Mayo Clinic Area

6. Baymont by Wyndham Kasson Rochester Area

7. Hilton Garden Inn Rochester Downtown, MN

8. Treasure Island Resort & Casino

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

10. Home2 Suites by Hilton Rochester Mayo Clinic Area

11. Spark by Hilton Rochester South

12. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

13. Candlewood Suites Rochester Mayo Clinic Area by IHG

14. Econo Lodge Mayo Clinic Area

15. Aspen Suites

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

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

18. AmericInn by Wyndham Rochester Near Mayo Clinic

19. Staybridge Suites Rochester - Mayo Clinic Area by IHG

20. Courtyard by Marriott Rochester Mayo Clinic Area/Saint Marys

Vacation Rentals in Southeast Minnesota

The Berkman

Broadway Plaza, Trademark Collection by Wyndham

Steps to Marina & Beach: Couples Cottage in Pepin

Downtown Northfield Apt: Winter Walk & Shops

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

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

EVEN Hotel Rochester - Mayo Clinic Area by IHG

St James Hotel, a Historic Hotel of America

Express Suites Riverport Inn & Suites

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

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Cobblestone Hotel & Suites - Austin

Brentwood Inn & Suites

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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