In 1829 he led a delegation to London, which included the Dominican priest John Pius Leahy and Edmund Ignatius Rice, founder of the Christian Brothers, to lobby the government over a clause in the Catholic Emancipation bill which would have prohibited the religious orders.
O'Connor was the chief negotiator with the Prime Minister and Home Secretary, and received an assurance that the clause would only be enforced by the attorney general – an action, they believed, that would never be taken.
He eventually he collected £942, including money from an Indian princess and a gift of £10 from the Catholic Marchioness Wellesley, of the viceregal lodge, Phoenix Park (sister-in-law to the Prime Minister).
He set sail for India on the Duke of Sussex (8 May 1835) from Gravesend, with his secretary and vicar general, Patrick Moriarty (1804–75), and several thousand books, on a journey that took ninety-three days by way of the Cape of Good Hope.
By 1836 the civil authorities recognised him as the leader of local Catholics and in turn he acted as a liaison between the Church and Presidency of Madras.
He also took a keen interest in the Repeal movement, visited Daniel O'Connell in Richmond prison in 1844, and celebrated a special Mass of thanksgiving on his release.