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

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 $146

CA $168 total

includes taxes & fees

Oct 18 - Oct 19

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 indoor pool area with lounge chairs and a pool.

A modern bar area with seating and a counter.

2. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Lucy

CA $168

CA $193 total

includes taxes & fees

Oct 17 - Oct 18

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 interior with a seating area, a bookshelf, and a window with a view of trees.

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

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.

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

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

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 $147

CA $169 total

includes taxes & fees

Nov 7 - Nov 8

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 laundry area with two Whirlpool washers and a dryer, a wooden shelf above, and a white ceiling.

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

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

5. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Phil

CA $109

CA $125 total

includes taxes & fees

Nov 8 - Nov 9

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.

6. Baymont by Wyndham Kasson Rochester Area

Kasson

Lynnette

CA $92

CA $99 total

includes taxes & fees

Oct 18 - Oct 19

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.

A breakfast bar with a wooden counter, a coffee machine, and a refrigerator.

7. 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.

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

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.

8. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

howard

CA $181

CA $208 total

includes taxes & fees

Oct 24 - Oct 25

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 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.

9. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $94

CA $108 total

includes taxes & fees

Nov 1 - Nov 2

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 hotel reception desk with a modern design, a clock, and a digital screen.

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

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

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

Kutzky Park

Jackie

CA $140

CA $161 total

includes taxes & fees

Oct 17 - Oct 18

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

A hotel room with a flat-screen TV, a sofa with a red pillow, a small table, and a lamp.

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.

11. TownePlace Suites by Marriott Rochester

Rochester

Terry

CA $139

CA $160 total

includes taxes & fees

Nov 8 - Nov 9

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 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.

12. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Christine

CA $162

CA $187 total

includes taxes & fees

Oct 10 - Oct 11

A modern hotel lobby with a reception desk, seating area, and a kitchenette.

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.

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

13. Spark by Hilton Rochester South

Rochester

Stanton

CA $120

CA $138 total

includes taxes & fees

Nov 8 - Nov 9

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 bar with wooden stools and a neon sign.

A hotel room with two beds, a desk, a chair, and a mirror.

14. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Jeanne

CA $104

CA $120 total

includes taxes & fees

Oct 25 - Oct 26

A spacious lobby with a reception desk, sofas, and a coffee table.

A hotel room with a large bed, a sofa, a TV, and a desk.

A Sleep Inn hotel with a covered entrance, stone pillars, and a clear blue sky.

An indoor swimming pool with clear blue water, surrounded by tiled flooring and equipped with a pool ladder.

15. Sleep Inn & Suites West-Near Medical Center

Rochester

Jacqueline

CA $119

CA $137 total

includes taxes & fees

Nov 1 - Nov 2

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 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.

16. Comfort Inn & Suites West - Medical Center

Rochester

yuan

CA $127

CA $147 total

includes taxes & fees

Nov 8 - Nov 9

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

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

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

17. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Sheri

CA $162

CA $190 total

includes taxes & fees

Oct 25 - Oct 26

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.

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

Kutzky Park

Janet

CA $156

CA $180 total

includes taxes & fees

Oct 17 - Oct 18

A modern restaurant with a central counter, seating area, and a clock on the wall.

A reception area with a stone wall, a flat-screen TV, a clock, and a seating area with patterned chairs.

A hotel room with a patterned carpet, a sofa, a small table, a microwave, and a refrigerator.

A hotel with a parking lot, multiple vehicles, and a well-maintained lawn.

19. Best Western Plus Albert Lea I-90/I-35 Hotel

Albert Lea

Michele

CA $119

CA $132 total

includes taxes & fees

Nov 8 - Nov 9

An indoor swimming pool with a curved design, surrounded by palm trees and a white pool ladder.

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.

A modern interior with a fireplace, a green armchair, and a patterned rug.

20. Treasure Island Resort & Casino

Welch

Bill

CA $122

CA $152 total

includes taxes & fees

Oct 13 - Oct 14

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Vacation Rentals in Southeast Minnesota

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 modern kitchen with wooden cabinets, a granite countertop, and a stainless steel stove.

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."

Aparthotel

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

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.

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

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.

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

Downtown Northfield Apt: Winter Walk & Shops

Northfield

"It was amazing!"

Apartment

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

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.

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."

Cottage

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

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.

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!"

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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

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

10/10 Excellent

"Twigs restaurant is fantastic! Staff is very accommodating, especially as a Mayo “visitor “ it was wonderful to have one less thing to worry about! This is the only place I stay now when I go to Rochester"

Brentwood Inn & Suites

10/10 Excellent

"Wonderful location with free parking and a nice free breakfast."

Hotel Indigo Rochester – Mayo Clinic Area by IHG

10/10 Excellent

"Great location. Great accommodations. Highly recommended."

Hyatt House Rochester/Mayo Clinic Area

10/10 Excellent

"The room was very clean. Staff were kind and pleasant upon check in."

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."

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

3595 Commercial Drive SW Rochester MN

CA $83

CA $95 total

Oct 22 - Oct 23

includes taxes & fees

7.6/10 Good! (89 reviews)

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $109

CA $121 total

Oct 14 - Oct 15

includes taxes & fees

Med City Inn & Suites - Mayo Clinic Area

435 16th Ave Nw Rochester MN

CA $108

CA $124 total

Oct 10 - Oct 11

includes taxes & fees

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

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $152

CA $169 total

Oct 14 - Oct 15

includes taxes & fees

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

CA $178

CA $205 total

Nov 6 - Nov 7

includes taxes & fees

8.8/10 Excellent! (1,003 reviews)

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. EVEN Hotel Rochester - Mayo Clinic Area by IHG

4. Hotel Indigo Rochester – Mayo Clinic Area by IHG

5. Comfort Inn & Suites Rochester South Mayo Clinic

6. Baymont by Wyndham Kasson Rochester Area

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

8. Home2 Suites by Hilton Rochester Mayo Clinic Area

9. Econo Lodge Mayo Clinic Area

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

11. TownePlace Suites by Marriott Rochester

12. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

13. Spark by Hilton Rochester South

14. AmericInn by Wyndham Rochester Near Mayo Clinic

15. Sleep Inn & Suites West-Near Medical Center

16. Comfort Inn & Suites West - Medical Center

17. Staybridge Suites Rochester - Mayo Clinic Area by IHG

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

19. Best Western Plus Albert Lea I-90/I-35 Hotel

20. Treasure Island Resort & Casino

Vacation Rentals in Southeast Minnesota

Broadway Plaza, Trademark Collection by Wyndham

The Berkman

Downtown Northfield Apt: Winter Walk & Shops

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

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Brentwood Inn & Suites

Hotel Indigo Rochester – Mayo Clinic Area by IHG

Hyatt House Rochester/Mayo Clinic Area

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

More cheap stays in Southeast Minnesota

Birch Hill Suite Rochester – Med City

Boarders Inn & Suites by Cobblestone Hotels - Faribault

Med City Inn & Suites - Mayo Clinic Area

Country Inn & Suites by Radisson, Albert Lea - Austin

Cobblestone Hotel & Suites - Austin

Brentwood Inn & Suites

Hotels in Southeast Minnesota with star rating

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