O'Brien continued to be active in the Chartist movement and in 1840 he was arrested and charged with making a seditious speech in Manchester. He was convicted of sedition and sentenced to eighteen months in Lancaster Prison. When O'Brien was released from prison he found it difficult to continue working with Feargus O'Connor. The two men disagreed over the issue of Physical Force. Another source of dispute concerned parliamentary elections. O'Brien favoured the idea of putting up Chartist candidates whereas O'Connor preferred the tactic of putting pressure on the Whig government by threatening to vote for Tory candidates. O'Brien was involved in standing Chartist candidates against Government Ministers in key seats, particularly in standing against Lord Palmerston in Tiverton.