One aspect of the company's operations was the Hudson's Bay Company Stores, trading posts that were established across northern Canada. Today, this is the only part of the company operation remaining, in the form of department stores under the name The Bay. The first department store opened in Winnipeg, Manitoba in 1881. Others soon followed. Many Hudson's Bay Company stores were, until quite recently, the only stores in remote towns. More recently, the stores in major downtown locations have been transformed into boutiques.

In 1970, on the 300th birthday of the company, head office functions were transferred from London, England to Winnipeg, Manitoba, Canada. As the company expanded into the east, head office functions were moved to Toronto, Ontario, Canada.

The Hudson's Bay Company building in MontrealToday there are five retail divisions: The Bay, Zellers, Home Outfitters, Designer Depot, and Fields.

Northern Stores are no longer operated by HBC, but by a corporation organized in 1987 under the name The North West Company. Simpson's department stores which were acquired by Hudson's Bay Company in 1979 were converted to The Bay stores in 1991. In the 1970s and 1980s, HBC operated a chain of catalogue stores under the name Shop-Rite. In these stores, little merchandise was displayed openly: customers made their selections from catalogues, and staff would retrieve the merchandise from storerooms. This form of retailing, now largely disappeared, was referred to as "catalogue showroom".

The legacy of the HBC has been maintained in part by the detailed record-keeping and archiving of material by the Company. Before 1974, the records of the HBC were kept in the London office headquarters. The HBC opened an Archives department to researchers in 1931. In 1974, the Hudson's Bay Company Archives were transferred from London to their Canadian headquarters in Winnipeg and granted public access to the collection the following year. In 1991 the archival records of the company were donated to the Manitoba Archives in Winnipeg, Manitoba.

In 1987 the HBC sold off its Canadian fur auction business to Hudson's Bay Fur Sales Canada (this company is now known as North American Fur Auctions). In 1991, the Bay agreed to stop selling fur in response to complaints from people opposed to killing animals for this purpose. However, in 1997, the Bay reopened its fur salons to meet the demand of consumers desiring to buy fur. Animal rights groups such as Freedom for Animals have been campaigning to get the Bay to once again stop selling fur.