Chakraborty, who has been with the team as assistant coach since July 2014, was at the helm of affairs during the Calcutta Football League Premier Division 2017, where they were pipped to the title by bitter foes East Bengal.
Mohun Bagan senior team will resume training tomorrow morning and post-training Chakraborty will interact with media, a statement read.
Sen stepped down as the chief coach minutes after they succumbed to a 1-2 defeat to a 10-man Chennai City FC, their first defeat of the season that came at their home ground.
Mohun Bagan have slipped to fifth place in standings after three draws and a loss as they next face defending champions Aizawl here on December 7.
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