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 reception desk with a large digital screen displaying a cityscape and the word "happy."

1. Hampton Inn & Suites Rochester-North

Rochester

Dr. Tim

CA $138

CA $159 total

includes taxes & fees

Oct 24 - Oct 25

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

2. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

Rici

CA $173

CA $219 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 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.

3. Comfort Inn & Suites West - Medical Center

Rochester

yuan

CA $123

CA $141 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 bar area with seating and a counter.

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.

4. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Kathy

CA $167

CA $193 total

includes taxes & fees

Oct 23 - Oct 24

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.

5. Spark by Hilton Rochester South

Rochester

Kimberly

CA $124

CA $142 total

includes taxes & fees

Nov 1 - Nov 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.

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

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

6. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

thomas

CA $152

CA $175 total

includes taxes & fees

Oct 23 - Oct 24

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

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

7. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Carrie

CA $146

CA $168 total

includes taxes & fees

Oct 14 - Oct 15

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 hotel room with a desk, a television mounted on the wall, a microwave, a lamp, a chair, and a refrigerator.

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

A swimming pool with a clear blue water surface, surrounded by a tiled deck and a few chairs.

8. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Darlene

CA $111

CA $128 total

includes taxes & fees

Nov 1 - Nov 2

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

A modern hotel building with a Staybridge Suites sign, multiple windows, and a parking lot.

9. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Sheri

CA $152

CA $178 total

includes taxes & fees

Oct 25 - Oct 26

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 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.

10. Hilton Garden Inn Rochester Downtown, MN

Downtown Rochester

John

CA $162

CA $186 total

includes taxes & fees

Oct 23 - Oct 24

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

11. Aspen Suites

Rochester

Dana

CA $201

CA $243 total

includes taxes & fees

Oct 2 - Oct 3

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

12. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

Vickie

CA $173

CA $200 total

includes taxes & fees

Oct 24 - Oct 25

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

A modern conference room with a long table, multiple chairs, and a wooden partition.

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

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

Kutzky Park

Jackie

CA $159

CA $183 total

includes taxes & fees

Nov 1 - Nov 2

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

A hotel room with a bed, a sink, a microwave, and a window with curtains.

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

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

14. Brentwood Inn & Suites

Downtown Rochester

Daniel

CA $133

CA $153 total

includes taxes & fees

Oct 2 - Oct 3

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.

15. Candlewood Suites Rochester Mayo Clinic Area by IHG

Rochester

Sean

CA $165

CA $190 total

includes taxes & fees

Oct 11 - Oct 12

A hotel breakfast area with a self-serve station, including a waffle maker, toaster, and various food items.

A hotel room with a large bed, bedside tables, a mirror, and a patterned carpet.

A compact kitchen with a microwave, refrigerator, and coffee maker. A small bar stool is near the counter.

A modern living room with a sofa, coffee table, and a TV mounted on a stone wall.

16. Quality Inn & Suites Mayo Clinic Area

Rochester

Edward

CA $109

CA $127 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 reception area with a reception desk, two armchairs, a clock, and a framed artwork on the wall.

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

A hotel room with a large window, a clock, a framed picture of pottery, a desk with a computer, and a seating area with patterned chairs.

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

Rochester

John

CA $97

CA $111 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 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.

18. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $100

CA $115 total

includes taxes & fees

Nov 1 - Nov 2

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.

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

19. TownePlace Suites by Marriott Rochester Mayo Clinic Area

Kutzky Park

Hafsa

CA $194

CA $224 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.

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

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

A modern kitchen with wooden cabinets, a microwave, an oven, and a dishwasher.

20. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Jeanne

CA $109

CA $126 total

includes taxes & fees

Oct 29 - Oct 30

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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.

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

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

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.

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

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

"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 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.

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 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.

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

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 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!"

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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

Kahler Grand Hotel

10/10 Excellent

"Check in staff was very helpful polite. Great experience all around."

Kahler Inn and Suites - Mayo Clinic Area

10/10 Excellent

"They are remodeling. They are doing a very nice job."

Treasure Island Resort & Casino

10/10 Excellent

"I liked the layout of the slot machines."

AmericInn by Wyndham Rochester Near Mayo Clinic

10/10 Excellent

"Our stay was great , free shuttle to Mayo Clinic was great!"

EVEN Hotel Rochester - Mayo Clinic Area by IHG

10/10 Excellent

"One of the cleanest hotels I’ve ever stayed in."

SpringHill Suites by Marriott Rochester-Mayo Clinic/St Marys

10/10 Excellent

"Had great help from staff."

Aspen Select

8/10 Good

"Really close to the st Mary's hospital. Parking was great"

Hyatt House Rochester/Mayo Clinic Area

10/10 Excellent

"."

Express Suites Riverport Inn & Suites

10/10 Excellent

"Friendly staff, quiet environment. My son particularly liked the pool."

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 $117 total

Oct 2 - Oct 3

includes taxes & fees

7.8/10 Good! (1,026 reviews)

Country Inn & Suites by Radisson, Albert Lea - Austin

2214 E Main St Albert Lea MN

CA $108

CA $120 total

Nov 1 - Nov 2

includes taxes & fees

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $109

CA $121 total

Oct 7 - Oct 8

includes taxes & fees

Brentwood Inn & Suites

123 Fourth Ave. NW Rochester MN

CA $133

CA $153 total

Oct 2 - Oct 3

includes taxes & fees

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $152

CA $169 total

Oct 11 - Oct 12

includes taxes & fees

Hotels in Southeast Minnesota with star rating

Explore a world of travel with Expedia

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. EVEN Hotel Rochester - Mayo Clinic Area by IHG

3. Comfort Inn & Suites West - Medical Center

4. Hyatt House Rochester/Mayo Clinic Area

5. Spark by Hilton Rochester South

6. Hotel Indigo Rochester – Mayo Clinic Area by IHG

7. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

8. Comfort Inn & Suites Rochester South Mayo Clinic

9. Staybridge Suites Rochester - Mayo Clinic Area by IHG

10. Hilton Garden Inn Rochester Downtown, MN

11. Aspen Suites

12. Home2 Suites by Hilton Rochester Mayo Clinic Area

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

14. Brentwood Inn & Suites

15. Candlewood Suites Rochester Mayo Clinic Area by IHG

16. Quality Inn & Suites Mayo Clinic Area

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

18. Econo Lodge Mayo Clinic Area

19. TownePlace Suites by Marriott Rochester Mayo Clinic Area

20. AmericInn by Wyndham Rochester Near Mayo Clinic

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

Kahler Grand Hotel

Kahler Inn and Suites - Mayo Clinic Area

Treasure Island Resort & Casino

AmericInn by Wyndham Rochester Near Mayo Clinic

EVEN Hotel Rochester - Mayo Clinic Area by IHG

SpringHill Suites by Marriott Rochester-Mayo Clinic/St Marys

Aspen Select

Hyatt House Rochester/Mayo Clinic Area

Express Suites Riverport Inn & Suites

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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