Boutique hotels in San Juan County

Find and book unique boutique hotels on Airbnb

Top-rated boutique hotels in San Juan County

Guests agree: these boutique hotels are highly rated for location, cleanliness and more.

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Guest favourite
A spacious bedroom features a large bed with soft linens, complemented by decorative pillows. Floor-to-ceiling windows provide panoramic views of the surrounding landscape, including trees and water. A small seating area with two chairs and a table is positioned near the glass doors.
Hotel room in Friday Harbor
4.96 out of 5 average rating, 23 reviews

Private suite w/ exceptional views & soaking tub

Your exceptional private suite awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian farm-style boutique inn, situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your luxurious suite atop the architectural award-winning Inn, complete with large bathroom and soaking tub, separate living area with kitchenette, modern amenities, and miles of trails, gardens, and natural beauty to explore. KING bedroom + DOUBLE sleeper sofa + Living area + bathroom.

Guest favourite
A modern guesthouse features a sloped roof and wooden exterior, set against a backdrop of tall evergreen trees. Large glass doors provide a view into the interior, blending harmoniously with the natural surroundings.
Hotel room in Friday Harbor
4.97 out of 5 average rating, 112 reviews

Private guesthouse immersed in nature

Your private guesthouse awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian-style, boutique inn situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your separate and private guesthouse with breathtaking views, modern amenities, and miles of trails, gardens, and natural beauty to explore. Private deck & floor-to-ceiling windows with a cozy & intimate woodsy view. Wheelchair accessible. KING bedroom + QUEEN loft + DOUBLE sleeper sofa + bathroom.

Top guest favourite
A vibrant room features a spacious bed adorned with a floral quilt, complemented by a cozy seating area with a gray sofa. Natural light flows through two windows, and decorative lamps illuminate handcrafted wooden trim. A colorful area rug adds warmth to the wood flooring.
Hotel room in Friday Harbor
5 out of 5 average rating, 15 reviews

Pine room at Juniper Lane 2 beds

Our Pine room is perfect for two people traveling together that want their own beds and a little more privacy, with the separate bathroom, located just a few feet across from your door. The room has a queen bed as well as a twin bunk (the twin beds are built into the wall with beams and are solid and independent of each other). The Pine room has a lovely view of the valley, beautifully handcrafted trim details made of rare, high altitude old-growth cedar, and knotty pine wainscoting.

Guest favourite
A modern guesthouse with a triangular roof is nestled among tall evergreen trees. The exterior showcases a contrasting black and warm wood facade, with large windows framed by nature. Surrounding wild grasses and shrubs create a serene, secluded atmosphere.
Hotel room in Friday Harbor
4.98 out of 5 average rating, 60 reviews

Private guesthouse surrounded by majestic firs

Your private guesthouse awaits at ~ Inn at Saltwater Farm ~ a modern, Scandinavian-style, boutique inn situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your separate and private guesthouse with breathtaking views, modern amenities, and miles of trails, gardens, and natural beauty to explore. Light & bright, private deck, floor-to-ceiling windows & an intimate woodsy view. KING bedroom + QUEEN loft + DOUBLE sleeper sofa + bathroom.

A cozy room features a wooden bunk bed with comfortable mattresses and a chair positioned by a large window. Natural light brightens the space, showcasing the earthy tones of the furnishings and the inviting view of greenery outside.
Hotel room in Friday Harbor
4.51 out of 5 average rating, 119 reviews

Wayfarers Guest House. Private, driftwood bunks #3

Thank you for finding the Wayfarers Rest, providing comfortable and convenient lodging for active travelers since 1999. Room 3 is a private room that can sleep up to 3, all linens provided. The common areas you will share with other guests (fully equipped kitchen, dining, living room and bathrooms) Wayfarers Rest is located just 4 blocks from the ferry terminal and two blocks from main St., easy walking. Free Wi-Fi, parking & chicken eggs. Pet friendly

Guest favourite
A well-appointed guest room is presented with a king sleigh bed positioned against a dark blue accent wall. Soft bedding complements the tranquil decor. A nightstand is included, along with a coffee station, enhancing the convenience for guests.
Hotel room in Lopez Island
4.88 out of 5 average rating, 51 reviews

~VintageLuxury~ SoakingTub Fireplace King Bed WiFi

✔ No Cleaning Fees ✔ Super Fast WIFI ✔ Fireplace ✔ Full Bathroom w. Soaking Tub ✔ In Room Coffee + Decaf & Tea ✔ Leather couch + King Sleigh Bed ✔ Access to All Common Spaces at Edenwild Boutique Hotel ✔ 24/7 Staff that are here when you need them and never when you don't :) ✔ TV Free Property- Bring your Tablet for Movies ✔ Free Parking Our commitment to you has made us TripAdvisors #1 Hotel in the San Juan Islands.

A modern barn structure is set against a vibrant sunset sky, featuring a blend of warm colors. Surrounding grassland is lush and green, dotted with trees in the background, creating a serene atmosphere. A small fire pit with seating is positioned nearby.
Hotel room in Friday Harbor
5 out of 5 average rating, 3 reviews

Unique private suite w/ forest & meadow views

Your unique 700+ sqft suite awaits at ~ at Saltwater Farm ~ a modern, Scandinavian farm-style abode, situated on 162 wild and beautiful acres just outside the town of Friday Harbor. Escape to your large private suite above our stunning new barn with kitchen, modern amenities, DSL WiFi internet, and miles of trails, gardens, and natural beauty to explore. KING bedroom + 2 DOUBLE sleeper sofa loft + TWIN bedroom + bathroom

Guest favourite
Hotel room in Lopez Island
4.86 out of 5 average rating, 35 reviews

•Walk to Everything• Wi-Fi •Island Hotel•

Your Suite awaits at ~The Edenwild Boutique Inn~ Island Vintage meets modern amenities. Think friendly, not stuffy with exceptional service. QUEEN Bed + Queen Sleeper Sofa. Bathroom with standup shower, plush towels and premium bath products. DIFFERENT than other AirBnBs where you feel like your crashing. We think of every aspect of your stay and our staff is always there when you need us and never when you don’t.

Top guest favourite
A vibrant sleeping area is highlighted by a spacious bed adorned with a colorful patterned blanket. The walls are painted in a deep hue, accented by wooden paneling. A cozy chair, a bedside lamp, and framed artwork complement the inviting atmosphere.
Hotel room in Friday Harbor
4.98 out of 5 average rating, 48 reviews

Cedar & Mandala two bedroom suite at Juniper Lane

Juniper Lane Guest House, a hip and unique boutique Inn on San Juan Island. This unique Friday Harbor accommodations is a custom crafted bold mosaic of exotic woods, tile, art, and color. Nestled on the edge of Friday Harbor overlooking Beaverton Valley it has a rural feel yet is still close to town. This Boutique Inn offers a variety of accommodations that are “brilliant and affordable” for everyone.

Top guest favourite
A serene beach scene is captured under a clear blue sky. Two figures stroll along the shoreline, with gentle waves lapping at the sandy beach. Sunlight filters through nearby trees, casting a soft glow on the landscape. The atmosphere reflects tranquility and natural beauty.
Hotel room in Lopez Island
4.94 out of 5 average rating, 50 reviews

Romantic Island Hotel with Breathtaking Sunsets

✔ Super Fast WIFI ✔ In Room Coffee + Decaf & Tea ✔ Full Bathroom ✔ Private Covered Porch ✔ Access to All Common Spaces at Edenwild Boutique Hotel ✔ 24/7 that are here when you need them and never when you don't :) ✔ Walk to shops, restaurants, and beaches. The Edenwild is a 10 room Boutique Hotel that is Elegant as well as friendly. Your privacy and comfort is our top priority.

Superhost
Hotel room in Lopez Island
4.91 out of 5 average rating, 107 reviews

•Sweet Island Hotel• Fireplace, Soaking Tub, WIFI

✔ Super Fast WIFI ✔ Fireplace ✔ In Room Coffee + Decaf & Tea ✔ Full Bathroom w. Soaking Tub ✔ 24/7 Staff That There When You Need Them and Never When You Don't :) ✔ Access to All Common Spaces at Edenwild Boutique Hotel ✔ Onsite Bicycle and Kayak rentals We think of every aspect of your stay, and our staff is always there when you need us and never when you don’t.

Superhost
A charming Victorian inn is showcased at twilight, featuring a sprawling front porch lined with warm lights. A brick pathway is adorned with blooming white flowers, leading to the welcoming entrance surrounded by lush greenery.
Hotel room in Lopez Island
4.88 out of 5 average rating, 32 reviews

•BoutiqueHotel• KingSuite •Waterviews • Fireplace•

Experience the best of both worlds—hotel amenities with the privacy of an Airbnb. This charming Victorian inn offers you an in-suite fireplace, vintage clawfoot tub, and easy access to nearby cafes and restaurants, all while giving you the space to unwind in total privacy. Escape the everyday and reconnect in a quiet seaside village, overlooking the bay.

Popular amenities for San Juan County boutique hotels