He was not excluded from Parliament during Pride's Purge on 20 December 1648 and declared his opposition to the earlier Commons vote accepting Charles I's answers in the Treaty of Newport as grounds for continuing negotiations.
In January 1649 he was appointed to sit as a commissioner at the trial of Charles I and sat for a total of six sessions.
Unlike his elder brother Thomas Chaloner, he did not sign the royal death warrant.
The London faction of the New Model Army arrested him, but on 7 December that year, as the London faction's star fell and Monck's rose, the Rump ordered Chaloner's release, and in January 1660 confirmed his governorship of the Isle of Man.
[2] His explanation was disregarded and he was among those whose property was sequestrated by the state under the "forfeitures not extending to Life" terms of the Act of Indemnity and Oblivion.