In the early 1980s, the MBTA suffered from a serious budget crisis, which resulted in service cuts.
MBTA Commuter Rail service to Providence and Concord and on the Woburn Branch were cut entirely, five underused commuter rail stations were closed, Boylston and Essex were closed for short periods, and the outer ends of the Orange and Blue lines were bustituted on Sundays.
Bowdoin, with low ridership and in close proximity to Government Center, was closed on January 3, 1981 due to budget cuts.
It reopened on January 11, 1982, but only on weekdays until 6:30 pm - intended to serve workers in nearby office and government buildings.
Bowdoin was briefly closed again from March 3 to April 20, 1982, and reopened again with limited hours, with Government Center serving as the terminus on nights and weekends (though trains continued to loop at Bowdoin).
After the early 1980s, it was the only MBTA subway station with limited hours.

The station was closed from July 29 to September 8, 1992, during track work on the loop.
As the MBTA planned the Blue Line Modernization Project in the early 1990s, the agency planned to close Bowdoin in order to eliminate the tight loop.
The closure would take place after the renovation of Government Center, which would re-add a long-closed entrance at the west end of the Blue Line platform.
In 2008, the MBTA began running six-car trains on the Blue Line.
Because the eastbound side of the Bowdoin platform can only fit four cars, the MBTA had originally planned to close the station when six-car trains entered service; a planned renovation of Government Center station was to add a second headhouse close to Bowdoin Square.
However, the station was kept open, with only four cars on each eastbound train  berthed at the platform.

Until at least 2011, the MBTA still planned to close the station after Government Center was renovated.
However, by 2013, the MBTA decided not to construct the planned west entrance at Government Center, and to instead build only a less-expensive emergency exit.
On December 28, 2013, the MBTA resumed night and weekend service to Bowdoin station.
The change was intended to provide alternative transportation during the three-month closure of the Callahan Tunnel and subsequent two-year closure of Government Center station.
This was the first time since 1981 that the station was open during all operating hours.
In February 2016, the MBTA announced that Bowdoin would remain open at all times even after Government Center reopened on March 21.
Daily ridership at the station increased from 1,526 in 2013 to 2,127 in FY 2019.

The reconstructions of Government Center in 2014–16 left Bowdoin as the only non-accessible metro station on the Blue Line; aside from street-level light rail stops, Bowdoin is one of only four non-accessible MBTA subway stations.
In 2019, the MBTA indicated that Bowdoin was a "Tier II" accessibility priority pending the results of conceptual design.
In the early 1980s, the MBTA suffered from a serious budget crisis, which resulted in service cuts. MBTA Commuter Rail service to Providence and Concord and on the Woburn Branch were cut entirely, five underused commuter rail stations were closed, Boylston and Essex were closed for short periods, and the outer ends of the Orange and Blue lines were bustituted on Sundays. Bowdoin, with low ridership and in close proximity to Government Center, was closed on January 3, 1981 due to budget cuts. It reopened on January 11, 1982, but only on weekdays until 6:30 pm - intended to serve workers in nearby office and government buildings. Bowdoin was briefly closed again from March 3 to April 20, 1982, and reopened again with limited hours, with Government Center serving as the terminus on nights and weekends (though trains continued to loop at Bowdoin). After the early 1980s, it was the only MBTA subway station with limited hours.
The station was closed from July 29 to September 8, 1992, during track work on the loop. As the MBTA planned the Blue Line Modernization Project in the early 1990s, the agency planned to close Bowdoin in order to eliminate the tight loop. The closure would take place after the renovation of Government Center, which would re-add a long-closed entrance at the west end of the Blue Line platform. In 2008, the MBTA began running six-car trains on the Blue Line. Because the eastbound side of the Bowdoin platform can only fit four cars, the MBTA had originally planned to close the station when six-car trains entered service; a planned renovation of Government Center station was to add a second headhouse close to Bowdoin Square. However, the station was kept open, with only four cars on each eastbound train  berthed at the platform.
Until at least 2011, the MBTA still planned to close the station after Government Center was renovated. However, by 2013, the MBTA decided not to construct the planned west entrance at Government Center, and to instead build only a less-expensive emergency exit. On December 28, 2013, the MBTA resumed night and weekend service to Bowdoin station. The change was intended to provide alternative transportation during the three-month closure of the Callahan Tunnel and subsequent two-year closure of Government Center station. This was the first time since 1981 that the station was open during all operating hours. In February 2016, the MBTA announced that Bowdoin would remain open at all times even after Government Center reopened on March 21. Daily ridership at the station increased from 1,526 in 2013 to 2,127 in FY 2019.
The reconstructions of Government Center in 2014–16 left Bowdoin as the only non-accessible metro station on the Blue Line; aside from street-level light rail stops, Bowdoin is one of only four non-accessible MBTA subway stations. In 2019, the MBTA indicated that Bowdoin was a "Tier II" accessibility priority pending the results of conceptual design.
Bowdoin station