Following a disgreement over the inclusion of the destitute in church congregations, in 1633 he resigned from the established church and moved to Holland. In 1637 he acquired the patent for a colony in Massachusetts and sailed with much his congregation for Boston. In March of 1638 he founded the colony on New Haven.
As a burgess, he held considerable political power in the new colony and continued to influence its development until his death of apoplexy in 1670.