Early life and education
Ames was born at Ipswich, and was brought up by a maternal uncle, Robert Snelling of Boxford. He was educated at the local grammar school and from 1594 at Christ's College, Cambridge. He was considerably influenced by his tutor at Christ's, William Perkins, and by his successor Paul Bayne. Ames graduated BA in 1598 and MA in 1601, and was chosen for a fellowship in Christ's College.
He was popular in the university, and in his own college. One of Ames's sermons became historical in the Puritan controversies. It was delivered in the university Church of St Mary the Great, Cambridge on 21 December 1609, and in it he rebuked sharply "lusory lotts" and the "heathenish debauchery" of the students during the Twelve Days of Christmas.
A partisan election, however, had led to the mastership at Christ's going to Valentine Carey. He quarrelled with Ames for disapproving of the surplice and other outward symbols. Ames's vehemence led to his being summoned before the Vice-Chancellor, who suspended him "from the exercise of his ecclesiastical function and from all degrees taken or to be taken."