Book The Best Hotels in Southeast Minnesota, MN for 2026 from CA $93 - 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 Comfort Inn & Suites hotel with a modern design, featuring a prominent signage and a parking lot.

1. Comfort Inn & Suites Rochester South Mayo Clinic

Rochester

LeeAnn

CA $123 total

includes taxes & fees

Dec 11 - Dec 12

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

2. Sleep Inn & Suites West-Near Medical Center

Rochester

Christopher

CA $120 total

includes taxes & fees

Dec 11 - Dec 12

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

3. Baymont by Wyndham Kasson Rochester Area

Kasson

Dana

CA $100 total

includes taxes & fees

Nov 22 - Nov 23

A hotel kitchen with a long counter, coffee machines, a bread display, and a fruit bowl.

4. Econo Lodge Mayo Clinic Area

Rochester

Britta

CA $110 total

includes taxes & fees

Dec 12 - Dec 13

A spacious outdoor dining area with multiple tables and chairs, large windows, and a wooden ceiling structure.

5. Hotel Indigo Rochester – Mayo Clinic Area by IHG

Downtown Rochester

Kathleen

CA $159 total

includes taxes & fees

Nov 28 - Nov 29

A modern dining area with high tables, chairs, and pendant lighting.

6. Hampton Inn & Suites Rochester-North

Rochester

Mark

CA $158 total

includes taxes & fees

Dec 11 - Dec 12

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

7. Hyatt House Rochester/Mayo Clinic Area

Downtown Rochester

Robert Blaise

CA $182 total

includes taxes & fees

Dec 11 - Dec 12

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

8. Comfort Inn & Suites West - Medical Center

Rochester

Angela

CA $135 total

includes taxes & fees

Dec 11 - Dec 12

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

9. Spark by Hilton Rochester South

Rochester

Jen

CA $110 total

includes taxes & fees

Nov 22 - Nov 23

A restaurant with wooden tables and bar stools, a bar area with a counter, and multiple televisions mounted on the walls.

10. AmericInn by Wyndham Rochester Near Mayo Clinic

Rochester

Madelyn

CA $120 total

includes taxes & fees

Dec 7 - Dec 8

11. Quality Inn near Medical Center

Rochester

B. Alice

CA $103 total

includes taxes & fees

Dec 3 - Dec 4

A Holiday Inn Express building with a covered entrance, multiple floors, and a parking lot.

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

Rochester

Rick

CA $131 total

includes taxes & fees

Dec 12 - Dec 13

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

13. Treasure Island Resort & Casino

Welch

Jacob

CA $152 total

includes taxes & fees

Nov 19 - Nov 20

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

14. EVEN Hotel Rochester - Mayo Clinic Area by IHG

Kutzky Park

Ashley

CA $206 total

includes taxes & fees

Dec 10 - Dec 11

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

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

Rochester

John

CA $114 total

includes taxes & fees

Nov 16 - Nov 17

A reception area with a wooden reception desk, a "Welcome to the Bread & Butter State" sign, and a "Please Center" sign.

16. Hampton Inn Rochester-South

Rochester

Susan

CA $159 total

includes taxes & fees

Dec 12 - Dec 13

An outdoor seating area with colorful striped sofas and yellow chairs, a fire pit, and a covered patio with string lights.

17. Home2 Suites by Hilton Rochester Mayo Clinic Area

Rochester

howard

CA $181 total

includes taxes & fees

Nov 29 - Nov 30

A modern living room with a fireplace, comfortable seating, and large windows.

18. Staybridge Suites Rochester - Mayo Clinic Area by IHG

Kutzky Park

Sheri

CA $175 total

includes taxes & fees

Nov 25 - Nov 26

A water slide with a frog theme, a pool, and a seating area with umbrellas.

19. Med City Inn & Suites - Mayo Clinic Area

Kutzky Park

Stephanie

CA $120 total

includes taxes & fees

Dec 14 - Dec 15

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

20. Centerstone Plaza Hotel Soldiers Field - Mayo Clinic Area

Historic Southwest

Jordan

CA $187 total

includes taxes & fees

Nov 24 - Nov 25

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Stay near popular Southeast Minnesota attractions

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.

See properties

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

A large, two-story Tudor-style house with a well-maintained lawn and a driveway leading to the entrance.

The Inn at Shattuck St. Mary's

Faribault

10/10 Excellent

Kailey

A table with a floral arrangement, a candle, and several ceramic mugs.

Alexander Mansion Bed and Breakfast

Historic Downtown Winona

10/10 Excellent

Al

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.

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

Kutzky Park

10/10 Excellent

Alexey

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

TownePlace Suites by Marriott Rochester Mayo Clinic Area

Kutzky Park

10/10 Excellent

Cory

A modern living room with a flat-screen TV, a fireplace, a sofa, a coffee table, and a view of a cityscape through large windows.

Hilton Rochester Mayo Clinic Area

Downtown Rochester

10/10 Excellent

Anonymous traveller

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

The Berkman

Folwell

10/10 Excellent

Absolutely beautiful property with great amenities...perfect for a 10 day stay, with everything you need to be self-sustained. Excellent dining choices very close like the Red Cow and the Canadian Honker restaurants...St Mary's Mayo is directly across the street with an active Shuttle to the other Mayo locations. This stay put my wife at ease during our visit. Such great staff, too. Thank you Nicole!

Jason