Cllr Chowdhary, who was elected to Reading Borough Council in 2008 but de-selected by the Conservatives for next month's elections, dramatically quit the Tory Party last week.
He stunned the year's final borough council meeting and also announced plans to sue key members of the Reading East Conservative Association, who he claimed made false allegations to the police in a bid to discredit him.
This week he said it has been a "privilege and pleasure" to serve the people of Peppard and he has decided to contest the seat as an independent after receiving "so much support and encouragement" from residents of all political persuasions.
Cllr Chowdhary, who is battling cancer, said: "Despite the corrosive internal politics currently within the Reading East Conservatives, I have always held strong Conservative values and will continue to do so whilst fighting for the right to continue to represent the residents of Peppard ward.
"I know that the Reading East Conservatives will fancy their chances of holding Peppard ward, but I am prepared for the fight.
"I am asking for people who would normally vote Conservative to recognise the injustice that has been done and make a stand against the Reading East Conservative Party who treated me so badly and put my young family through hell."
He has received the backing of Marie Rogers, former chairman of Conservative Peppard Branch Committee, and its former secretary, Trish Flinn, who both resigned following his deselection.