Earlier on Saturday morning, Chowdhury announced he was withdrawing from the Rejinagar bypoll, citing harassment of party workers and the absence of an official symbol.
He claimed that workers were being harassed, causing many to leave the area for work, and that the party lacked a symbol, complicating the contest.
By afternoon, Chowdhury reversed course after a private meeting with senior leaders of the Mamata Banerjee faction, including Mamata herself, who urged him to stay.
The decision comes amid an Election Commission order that froze the Trinamool symbol, forcing the faction to adopt the "Football Player" symbol as part of a temporary name change to Mamata All India Trinamool Congress.
Local farm labourer Arun Kumar, who had joined the party's campaign, said the sudden change gave him hope to fight against the ruling party's influence.
Chowdhury will now submit his nomination papers by the September 30 deadline, setting the stage for the Oct 6 vote.