In November 1928, the Northern Pacific District Engineer was advocating for a new depot. Meanwhile, an energetic new manager operated the Mandan lunchroom, which earned the railroad between $1,000 and $1,500 in monthly net profit by attracting local customers despite occupying a building described as "old, inadequate, and in need of repair." Northern Pacific included a new lunchroom in its 1929 reconstruction budget. One executive objected that a separate restaurant would compete with Mandan businesses, but the company approved it.
The original depot lunchroom stood east of the former Queen Anne-style depot. The new lunchroom was built west of the Colonial depot, allowing the earlier lunchroom to become an express-baggage area serving increased cargo traffic on the newly opened north and south branch lines. Demand became so great that the railroad also built a new brick freight house farther west along Main Street.
The depot and lunchroom project also included a 1,000-ton refrigerator-style icehouse for passenger-train service. It stood southeast of Main Street and Second Avenue NW, east of the park and service building.
The Beanery was modified several times. A basement water-softening plant installed in 1930 supplied the depot, lunchroom, and passenger cars. It was removed in 1942 when the complex connected to city water. Air conditioning was installed in 1936, partly because a competing coffee shop across the street installed it that year.
A vestibule was built outside the front door in 1943. Heavy wartime travel caused congestion near the magazine stand and cashier and excessive heat loss as passengers entered and left. In 1947, increased use of the basement restrooms—because depot restrooms were locked between trains—led to construction of new restrooms east of the lunchroom. When the Northern Pacific power plant was retired in 1959, a gas-fired basement boiler was installed to heat the lunchroom, depot, freight house, and nearby buildings.
The City of Mandan bought the Beanery and depot in 1988. Both had stood vacant for 10 years after Amtrak suspended passenger service in south-central and southwestern North Dakota.
In 2008, Beanery space was leased to the Mandan Historical Society for a museum, the Mandan Art Association for a gallery, and the Mandan Progress Association for offices. The Historical Society's lease was terminated in 2011 to provide more gallery space. In 2013, the Art Association downsized to accommodate a confectionery and pastry business, then closed its operation in 2014. The Five Nations Art store, operated by the Fort Abraham Lincoln Foundation, moved from the depot to the Beanery in 2017.
Much of this history comes from Lorenz P. Schrenk's article in the Northern Pacific Railway Historical Association's Mainstreeter, volume 16, number 3 (summer 1997). Construction details also come from Lowry Smith's article "Colonial Design Embodied in New NP Station" in the January 24, 1931, issue of Railway Age.