I stayed 3 nights at The Sophia Hotel (former Pickwick hotel, located at Broadway and Front that was just recently remodeled). Since this was an old hotel that was remodeled the rooms are pretty small but they have used the space well. They have comforatable beds, provide plenty of storage (closet, drawers) and have a mini fridge, and microwave. The hotel will soon have a restaurant as well but was under construction during our stay.
The Sophia hotel is also pet friendly at a very affordable rate!!! A huge plus if you want to travel with your pet. They don't provide pet amenities (bring your own bowls and bed) but for our 2 dogs it was a very comforatable stay (we have 1 small dog and a medium dog).
The location of this hotel is convenient as well, right by Horton Plaza, about 4-5 blocks from the Gaslamp and 1/2 mile to Seaport Village, perfect for checking out nightlife and restaurants. Its also close to the freeway and easy to access the beach
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