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 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 18 - Oct 19

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

A hotel room with a blue sofa, a wooden coffee table, a bed with white linens, a TV, and a large mirror.

2. 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 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.

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

3. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Jeanne

CA $109

CA $125 total

includes taxes & fees

Oct 29 - Oct 30

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.

4. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

Rici

CA $173

CA $218 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 modern reception area with a wooden reception desk, glass pendant lights, and a long hallway with seating.

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

5. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Carrie

CA $143

CA $164 total

includes taxes & fees

Oct 12 - Oct 13

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 indoor pool area with lounge chairs and a pool.

A modern bar area with seating and a counter.

6. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Kathy

CA $167

CA $192 total

includes taxes & fees

Oct 23 - Oct 24

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

A hotel room with a flat-screen TV mounted on the wall, a desk with a chair, a lamp, and a view of the city through the window.

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

7. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

Darlene

CA $121

CA $140 total

includes taxes & fees

Oct 29 - Oct 30

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

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.

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

8. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

thomas

CA $151

CA $174 total

includes taxes & fees

Oct 24 - Oct 25

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.

9. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

Vickie

CA $173

CA $199 total

includes taxes & fees

Oct 24 - Oct 25

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

10. Spark by Hilton Rochester South

Rochester

Kimberly

CA $127

CA $146 total

includes taxes & fees

Oct 9 - Oct 10

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

A hotel room with a bed, desk, chair, and a bathroom.

A modern hotel room with a wooden desk, orange chair, dark sofa, and a small table.

A modern breakfast area with a counter displaying various food items, a water dispenser, and a sign indicating a bakery section.

11. Holiday Inn Express Rochester South - Mayo Area by IHG

Rochester

Melissa

CA $136

CA $157 total

includes taxes & fees

Oct 18 - Oct 19

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

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

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.

12. Aspen Suites

Rochester

Dana

CA $201

CA $243 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 modern indoor swimming pool with seating areas and a city view.

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

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

13. Hilton Rochester Mayo Clinic Area

Downtown Rochester

Raymond

CA $255

CA $293 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 a kitchen area, a bed, a TV, and a seating area.

A modern kitchen with black cabinets, white countertops, and a tiled backsplash. There are pendant lights, a refrigerator, and a coffee machine.

A modern kitchen with a microwave, sink, and granite countertop.

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

Rochester

Vicky

CA $140

CA $161 total

includes taxes & fees

Oct 9 - Oct 10

A swimming pool with clear blue water, surrounded by lounge chairs and a view of residential buildings through large windows.

An outdoor patio area with wicker furniture, a central fire feature, and a stone building in the background.

A modern hotel with a flat roof, multiple windows, and a covered outdoor seating area.

A modern lounge area with seating, a fireplace, and a bar area.

15. Residence Inn by Marriott Rochester Mayo Clinic Area South

Rochester

Chee

CA $187

CA $215 total

includes taxes & fees

Oct 17 - Oct 18

A spacious hotel lobby with multiple seating areas, including sofas and round tables, and a large dining area with yellow chairs.

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.

A grocery store with refrigerated and frozen sections, shelves stocked with snacks, and a variety of beverages.

16. Hilton Garden Inn Rochester Downtown, MN

Downtown Rochester

John

CA $161

CA $186 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 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 hotel lobby with a reception desk, a digital information kiosk, and a patterned floor.

17. Treasure Island Resort & Casino

Welch

Bill

CA $103

CA $130 total

includes taxes & fees

Oct 26 - Oct 27

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

18. Econo Lodge Mayo Clinic Area

Rochester

Ashley

CA $100

CA $115 total

includes taxes & fees

Oct 25 - Oct 26

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.

An outdoor seating area with tables and chairs, a neon sign, and flower arrangements.

19. TownePlace Suites by Marriott Rochester Mayo Clinic Area

Kutzky Park

Hafsa

CA $194

CA $223 total

includes taxes & fees

Oct 23 - Oct 24

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

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.

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

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

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

Rochester

John

CA $99

CA $113 total

includes taxes & fees

Oct 5 - Oct 6

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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 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

"Excellent service and wonderful room!"

Apartment

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

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

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.

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 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.

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

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.

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 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 kitchen with wooden cabinets, a stove, a sink, and a window 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

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

Kahler Grand Hotel

10/10 Excellent

"Kendra at the front desk was warm and friendly. She does an outstanding job and make you feel very welcome."

Treasure Island Resort & Casino

8/10 Good

"We had a lot of fun. We always do. Rooms were great. Was first time we have ever had to wait for a room which was a little bit of a pain so we went and played bingo.. which was also fun however we did learn that the cater more to the electronic players then the paper card players. The numbers are called way too fast to actually be able to call your bingo before the next letter is called unless you’re playing electronic. Was still fun though."

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

10/10 Excellent

"Had an amazing stay while we were in Rochester for Mayo. The staff was very helpful. Had an excellent breakfast every morning and the attached restaurant Twigs is top notch. The rooms were clean and restocked every morning for our five day stay. The shuttle service is amazing. We don’t know what we would’ve done without it. The drivers were amazing. Very friendly and respectful. I will definitely stay he whenever we come back to Rochester. Thank you for a stress free stay during a difficult time for our family."

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

"."

AmericInn by Wyndham Rochester Near Mayo Clinic

8/10 Good

"very good restaurant attached with good food at a good price...and you get a 15% discount if you are also staying at the hotel."

Hotel Indigo Rochester – Mayo Clinic Area by IHG

8/10 Good

"Rooms were very clean and easy to manage. find the hotel was difficult"

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

7.8/10 Good! (85 reviews)

Med City Inn & Suites - Mayo Clinic Area

435 16th Ave Nw Rochester MN

CA $101

CA $116 total

Sep 30 - Oct 1

includes taxes & fees

Boarders Inn & Suites by Cobblestone Hotels - Faribault

1801 Lavender Dr Faribault MN

CA $108

CA $119 total

Oct 1 - Oct 2

includes taxes & fees

Country Inn & Suites by Radisson, Albert Lea - Austin

2214 E Main St Albert Lea MN

CA $115

CA $128 total

Oct 25 - Oct 26

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! (1,000 reviews)

Cobblestone Hotel & Suites - Austin

1000 16th Avenue NW Austin MN

CA $151

CA $168 total

Oct 14 - Oct 15

includes taxes & fees

8.8/10 Excellent! (814 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 $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. Comfort Inn & Suites West - Medical Center

3. AmericInn by Wyndham Rochester Near Mayo Clinic

4. EVEN Hotel Rochester - Mayo Clinic Area by IHG

5. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

6. Hyatt House Rochester/Mayo Clinic Area

7. Comfort Inn & Suites Rochester South Mayo Clinic

8. Hotel Indigo Rochester – Mayo Clinic Area by IHG

9. Home2 Suites by Hilton Rochester Mayo Clinic Area

10. Spark by Hilton Rochester South

11. Holiday Inn Express Rochester South - Mayo Area by IHG

12. Aspen Suites

13. Hilton Rochester Mayo Clinic Area

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

15. Residence Inn by Marriott Rochester Mayo Clinic Area South

16. Hilton Garden Inn Rochester Downtown, MN

17. Treasure Island Resort & Casino

18. Econo Lodge Mayo Clinic Area

19. TownePlace Suites by Marriott Rochester Mayo Clinic Area

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

Vacation Rentals in Southeast Minnesota

The Berkman

Steps to Marina & Beach: Couples Cottage in Pepin

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

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

Kahler Grand Hotel

Treasure Island Resort & Casino

Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

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

AmericInn by Wyndham Rochester Near Mayo Clinic

Hotel Indigo 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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